diff --git a/lib/layouts/jss.layout b/lib/layouts/jss.layout
index 0aab2aedb0..b0a7ec4373 100644
--- a/lib/layouts/jss.layout
+++ b/lib/layouts/jss.layout
@@ -126,7 +126,7 @@ Style "Short Title"
 	LabelString			"Short Title:"
 End
 
-InsetLayout "Flex:pkg"
+InsetLayout "Flex:Pkg"
 	LyxType				custom
 	LabelString			pkg
 	LatexType			command
@@ -146,14 +146,13 @@ InsetLayout "Flex:pkg"
 	  Color				latex
 	  Size				Small
 	EndFont
-	InToc				true
 	HTMLTag				pkg
 	ResetsFont			true
 	spellcheck			false
 End
 
-InsetLayout "Flex:proglang"
-	CopyStyle			"Flex:pkg"
+InsetLayout "Flex:Proglang"
+	CopyStyle			"Flex:Pkg"
 	LabelString			proglang
 	LatexName			proglang
 	Font
@@ -167,8 +166,8 @@ InsetLayout "Flex:proglang"
 	HTMLTag				proglang
 End
 
-InsetLayout "Flex:code"
-	CopyStyle			"Flex:proglang"
+InsetLayout "Flex:Code"
+	CopyStyle			"Flex:Proglang"
 	Spellcheck			0
 	LabelString			code
 	LatexName			code
@@ -182,10 +181,31 @@ InsetLayout "Flex:E-mail"
 	HTMLTag				email
 End
 
-Style "Code Chunk"
-	Category			MainText
+InsetLayout "Flex:Code Chunk"
+	CopyStyle			"Flex:Pkg"
 	LatexType			Environment
 	LatexName			CodeChunk
+	Decoration			Classic
+	Spellcheck			0
+	ParbreakIsNewline	1
+	FreeSpacing			1
+	PassThru			1
+	KeepEmpty			1
+	LabelString			"Code Chunk"
+	Font
+	  Family			Typewriter
+	EndFont
+	LabelFont
+	  #Series			Bold
+	  Color				Green
+	EndFont
+End
+
+Style "Code"
+	LatexName			Code
+	LabelString			"Code"
+	LatexType			Environment
+	LatexName			Code
 	Spellcheck			0
 	NextNoIndent		1
 	ParbreakIsNewline	1
@@ -193,12 +213,11 @@ Style "Code Chunk"
 	PassThru			1
 	KeepEmpty			1
 	NewLine				0
-	TopSep				0.7
-	BottomSep			0.7
+	TopSep				0
+	BottomSep			0
 	Align				Block
 	AlignPossible		Block
 	Labeltype			Above
-	LabelString			"Code Chunk"
 	Font
 	  Family			Typewriter
 	EndFont
@@ -210,22 +229,14 @@ Style "Code Chunk"
 	HTMLItem			p
 End
 
-Style "Standard Code"
-	CopyStyle			"Code Chunk"
-	LatexName			Code
-	LabelString			"Code"
-	TopSep				0
-	BottomSep			0
-End
-
 Style "Code Input"
-	CopyStyle			"Standard Code"
+	CopyStyle			"Code"
 	LatexName			CodeInput
 	LabelString			"Code Input"
 End
 
 Style "Code Output"
-	CopyStyle			"Standard Code"
+	CopyStyle			"Code"
 	LatexName			CodeOutput
 	LabelString			"Code Output"
 End
diff --git a/lib/lyx2lyx/lyx_2_2.py b/lib/lyx2lyx/lyx_2_2.py
index d9d64e6f8f..6e237fba4b 100644
--- a/lib/lyx2lyx/lyx_2_2.py
+++ b/lib/lyx2lyx/lyx_2_2.py
@@ -1223,7 +1223,7 @@ def revert_jss(document):
       while m != -1 or j != -1 or h != -1 or k != -1 or n != -1:
         # \pkg
         if h != -1:
-          h = find_token(document.body, "\\begin_inset Flex pkg", h)
+          h = find_token(document.body, "\\begin_inset Flex Pkg", h)
         if h != -1:
           endh = find_end_of_inset(document.body, h)
           document.body[endh - 2 : endh + 1] = put_cmd_in_ert("}")
@@ -1231,7 +1231,7 @@ def revert_jss(document):
           h = h + 5
         # \proglang
         if m != -1:
-          m = find_token(document.body, "\\begin_inset Flex proglang", m)
+          m = find_token(document.body, "\\begin_inset Flex Proglang", m)
         if m != -1:
           endm = find_end_of_inset(document.body, m)
           document.body[endm - 2 : endm + 1] = put_cmd_in_ert("}")
@@ -1239,12 +1239,16 @@ def revert_jss(document):
           m = m + 5
         # \code
         if j != -1:
-          j = find_token(document.body, "\\begin_inset Flex code", j)
+          j = find_token(document.body, "\\begin_inset Flex Code", j)
         if j != -1:
-          endj = find_end_of_inset(document.body, j)
-          document.body[endj - 2 : endj + 1] = put_cmd_in_ert("}")
-          document.body[j : j + 4] = put_cmd_in_ert("\\code{")
-          j = j + 5
+          # assure that we are not in a Code Chunk inset
+          if document.body[j][-1] == "e":
+              endj = find_end_of_inset(document.body, j)
+              document.body[endj - 2 : endj + 1] = put_cmd_in_ert("}")
+              document.body[j : j + 4] = put_cmd_in_ert("\\code{")
+              j = j + 5
+          else:
+              j = j + 1
         # \email
         if k != -1:
           k = find_token(document.body, "\\begin_inset Flex E-mail", k)
@@ -1378,28 +1382,14 @@ def revert_jss(document):
       while m != -1 or j != -1 or h != -1 or k != -1:
         # \CodeChunk
         if h != -1:
-          h = find_token(document.body, "\\begin_layout Code Chunk", h)
+          h = find_token(document.body, "\\begin_inset Flex Code Chunk", h)
         if h != -1:
-          endh = find_end_of_layout(document.body, h)
-          begindeeper = find_token(document.body, "\\begin_deeper", h)
-          enddeeper = find_token(document.body, "\\end_deeper", h)
-          document.body[enddeeper + 1 : enddeeper] = ["\\end_layout"]
-          document.body[enddeeper : enddeeper + 1] = put_cmd_in_ert("\\end{CodeChunk}")
-          del document.body[begindeeper]
+          endh = find_end_of_inset(document.body, h)
+          document.body[endh + 1 : endh] = ["\\end_layout"]
+          document.body[endh : endh + 1] = put_cmd_in_ert("\\end{CodeChunk}")
           document.body[h : h + 3] = put_cmd_in_ert("\\begin{CodeChunk}")
           document.body[h - 1 : h] = ["\\begin_layout Standard"]
           h = h + 1
-        # \Code
-        if m != -1:
-          m = find_token(document.body, "\\begin_layout Standard Code", m)
-        if m != -1:
-          endm = find_end_of_layout(document.body, m)
-          document.body[endm : endm + 1] = ["\\end_layout", "", "\\begin_layout Standard"]
-          document.body[endm + 3 : endm + 4] = put_cmd_in_ert("\\end{Code}")
-          document.body[endm + 13 : endm + 13] = ["\\end_layout", "", "\\begin_layout Standard"]
-          document.body[m + 1 : m] = ["\\end_layout", "", "\\begin_layout Standard"]
-          document.body[m : m + 1] = put_cmd_in_ert("\\begin{Code}")
-          m = m + 1
         # \CodeInput
         if j != -1:
           j = find_token(document.body, "\\begin_layout Code Input", j)
@@ -1422,6 +1412,17 @@ def revert_jss(document):
           document.body[k + 1 : k] = ["\\end_layout", "", "\\begin_layout Standard"]
           document.body[k : k + 1] = put_cmd_in_ert("\\begin{CodeOutput}")
           k = k + 1
+        # \Code
+        if m != -1:
+          m = find_token(document.body, "\\begin_layout Code", m)
+        if m != -1:
+          endm = find_end_of_layout(document.body, m)
+          document.body[endm : endm + 1] = ["\\end_layout", "", "\\begin_layout Standard"]
+          document.body[endm + 3 : endm + 4] = put_cmd_in_ert("\\end{Code}")
+          document.body[endm + 13 : endm + 13] = ["\\end_layout", "", "\\begin_layout Standard"]
+          document.body[m + 1 : m] = ["\\end_layout", "", "\\begin_layout Standard"]
+          document.body[m : m + 1] = put_cmd_in_ert("\\begin{Code}")
+          m = m + 1
 
 
 def convert_subref(document):
diff --git a/lib/templates/JSS-article.lyx b/lib/templates/JSS-article.lyx
index 3a257956ed..bdb0fa5cb7 100644
--- a/lib/templates/JSS-article.lyx
+++ b/lib/templates/JSS-article.lyx
@@ -214,7 +214,7 @@ nojss
 
 \begin_layout Title
 A Capitalized Title: Something about a Package 
-\begin_inset Flex pkg
+\begin_inset Flex Pkg
 status open
 
 \begin_layout Plain Layout
@@ -280,7 +280,7 @@ optional
 \end_layout
 
 \begin_layout Short Title
-\begin_inset Flex pkg
+\begin_inset Flex Pkg
 status open
 
 \begin_layout Plain Layout
@@ -315,7 +315,7 @@ e abstract of the article.The abstract of the article.The abstract of the
 
 \begin_layout Keywords
 keywords, comma-separated, not capitalized, 
-\begin_inset Flex proglang
+\begin_inset Flex Proglang
 status open
 
 \begin_layout Plain Layout
@@ -412,7 +412,7 @@ Fax: +43/512/507-2851
 
 \begin_layout Section
 About package 
-\begin_inset Flex pkg
+\begin_inset Flex Pkg
 status open
 
 \begin_layout Plain Layout
@@ -422,7 +422,7 @@ foo
 \end_inset
 
  in 
-\begin_inset Flex proglang
+\begin_inset Flex Proglang
 status open
 
 \begin_layout Plain Layout
@@ -458,7 +458,7 @@ The short title provides bookmarks for PDF files
 The special JSS style commands related to software and mathematical formulas
  are written as follows in \SpecialChar LyX
 : 
-\begin_inset Flex proglang
+\begin_inset Flex Proglang
 status open
 
 \begin_layout Plain Layout
@@ -468,7 +468,7 @@ R
 \end_inset
 
  or 
-\begin_inset Flex proglang
+\begin_inset Flex Proglang
 status open
 
 \begin_layout Plain Layout
@@ -478,7 +478,7 @@ R
 \end_inset
 
  for the names of programming languages, 
-\begin_inset Flex pkg
+\begin_inset Flex Pkg
 status open
 
 \begin_layout Plain Layout
@@ -488,7 +488,7 @@ foo
 \end_inset
 
  or 
-\begin_inset Flex pkg
+\begin_inset Flex Pkg
 status open
 
 \begin_layout Plain Layout
@@ -498,7 +498,7 @@ foo
 \end_inset
 
  for software packages, and 
-\begin_inset Flex code
+\begin_inset Flex Code
 status open
 
 \begin_layout Plain Layout
@@ -508,7 +508,7 @@ some code
 \end_inset
 
  or 
-\begin_inset Flex pkg
+\begin_inset Flex Pkg
 status open
 
 \begin_layout Plain Layout
@@ -588,54 +588,68 @@ Prob
 Writing several lines of code:
 \end_layout
 
-\begin_layout Code Chunk
+\begin_layout Standard
+\begin_inset Flex Code Chunk
+status open
 
-\end_layout
+\begin_layout Code
 
-\begin_deeper
-\begin_layout Standard Code
 first line of code
 \end_layout
 
-\begin_layout Standard Code
+\begin_layout Code
+
 second line of code
 \end_layout
 
-\begin_layout Standard Code
+\begin_layout Code
+
 third line of code
 \end_layout
 
-\end_deeper
+\end_inset
+
+
+\end_layout
+
 \begin_layout Standard
 Alternatively, you can distinguish between input and output code:
 \end_layout
 
-\begin_layout Code Chunk
+\begin_layout Standard
+\begin_inset Flex Code Chunk
+status open
 
-\end_layout
-
-\begin_deeper
 \begin_layout Code Input
+
 first line of input code
 \end_layout
 
 \begin_layout Code Input
+
 second line of input code
 \end_layout
 
 \begin_layout Code Output
+
 first line of output code
 \end_layout
 
 \begin_layout Code Output
+
 second line of output code
 \end_layout
 
 \begin_layout Code Output
+
 third line of output code
 \end_layout
 
-\end_deeper
+\end_inset
+
+
+\end_layout
+
 \begin_layout Section*
 Acknowledgments
 \end_layout