dmbortz wrote:
> Does anyone have any idea of how to fix this?

Could you try if the attached layout file works better?

Jürgen
#% Do not delete the line below; configure depends on this
#  \DeclareLaTeXClass{article (SIAM)}
# AMS-Article textclass definition file. Taken from initial LyX source code
# and from the Article textclass definition file, following the AMS sample
# paper "testmath.tex" of January, 1995
# Author : David L. Johnson <d...@lehigh.edu>
# Probably broken by Jean-Marc Lasgouttes <jean-marc.lasgout...@inria.fr>
# modified and modularized by Emmanuel GUREGHIAN <gureg...@boston.bertin.fr>
# Tinkered with Sep. '07 by Paul Rubin <ru...@msu.edu>
# Modified from  amsart.layout May '08 by Andrew Corrigan <acorr...@gmu.edu>


Format 11
Columns                 1
Sides                   2
PageStyle               Headers
Provides makeidx        1
Provides amsthm         1


ClassOptions
        FontSize   8|9|10|11|12
End

# We need to load the module this way 
# so we can disable some layouts below.
Input theorems-ams.module
ProvidesModule theorems-ams
ExcludesModule theorems-ams-extended

Style Standard
        Category              MainText
        Margin                Static
        LatexType             Paragraph
        LatexName             dummy
        ParIndent             MM
        ParSkip               0.4
        Align                 Block
        AlignPossible         Block, Left, Right, Center
        LabelType             No_Label
End


Preamble
\newcommand\eqref[1]{(\ref{#1})}
EndPreamble


Input stdsections.inc
Input stdstarsections.inc
Input lyxmacros.inc
Input stdlayouts.inc
Input stdlists.inc
Input stdfloats.inc
Input stdcounters.inc

Input amsdefs.inc

#
# some redefinitions of the AMS Theorems
#
Style Theorem
        LatexName             theorem
        Preamble
        EndPreamble
End

Style Theorem*
        Obsoletedby           Theorem
End

Style Corollary
        LatexName             corollary
        Preamble
        EndPreamble
End

Style Corollary*
        Obsoletedby           Corollary
End

Style Lemma
        LatexName             lemma
        Preamble
        EndPreamble
End

Style Lemma*
        Obsoletedby           Lemma
End

Style Proposition
        LatexName             proposition
        Preamble
        EndPreamble
End

Style Proposition*
        Obsoletedby           Proposition
End

Style Conjecture
        Preamble
        EndPreamble
End

Style Conjecture*
        Obsoletedby          Conjecture
End

Style Algorithm
        Category              Theorem
        Preamble
        EndPreamble
End

Style Algorithm*
        Obsoletedby          Algorithm
End

Style Definition
        LatexName            definition
        Preamble
        EndPreamble
End

Style Definition*
        Obsoletedby          Definition
End

Style AMS
        Obsoletedby          Subjectclass
End


NoStyle Fact
NoStyle Fact*
NoStyle Example
NoStyle Example*
NoStyle Problem
NoStyle Problem*
NoStyle Exercise
NoStyle Exercise*
NoStyle Remark
NoStyle Remark*
NoStyle Claim
NoStyle Claim*


Style Proof
        Margin                First_Dynamic
        LatexType             Environment
        LatexName             proof
        NextNoIndent          1
        OptionalArgs          1
        LabelSep              xx
        ParIndent             MMM
        ParSkip               0.4
        ItemSep               0.2
        TopSep                0.7
        BottomSep             0.7
        ParSep                0.3
        Align                 Block
        AlignPossible         Block, Left
        LabelType             Static
        LabelString           "Proof."
        EndLabelType          Box
        Font
          Shape               Up
          Size                Normal
        EndFont
        LabelFont
          Shape               Italic
        EndFont
        # We don't want the preamble from Theorem
        Preamble
        EndPreamble
End


### Now the title stuff. We do not use stdstruct.inc to keep
### things in the right order
Style Title
        Margin                Static
        LatexType             Command
        InTitle               1
        LatexName             title
        ParSkip               0.4
        ItemSep               0
        TopSep                0
        BottomSep             1
        ParSep                1
        Align                 Center
        LabelType             No_Label
        OptionalArgs          1
        Font
          Shape               Smallcaps
          Series              Bold
          Size                Larger
        EndFont
End


Style Author
        Margin                Static
        LatexType             Command
        InTitle               1
        LatexName             author
        LabelSep              xxx
        ParSkip               0.4
        TopSep                1.3
        BottomSep             0.7
        ParSep                0.7
        Align                 Center
        LabelType             No_Label
        Font
          Size                Large
          Shape               Smallcaps
        EndFont
End


Style Date
        Margin                Dynamic
        LatexType             Command
        InTitle               1
        LatexName             date
        LabelSep              xxx
        ParSkip               0.4
        TopSep                0.9
        BottomSep             0.5
        ParSep                1
        Align                 Center
        LabelType             Static
        LabelString           "Date:"
        Font
          Size                Large
        EndFont
        LabelFont
          Shape               Italic
          Size                Large
        EndFont
End


Style Abstract
        Margin                First_Dynamic
        LatexType             Environment
        InTitle               0
        LatexName             abstract
        LeftMargin            MMM
        LabelIndent           MMM
        RightMargin           MMM
        ParIndent             MM
        TopSep                0.7
        BottomSep             0.7
        Align                 Block
        LabelType             Static
        LabelString           "Abstract."
        LabelSep              M
        Font
          Size                Small
        EndFont
        LabelFont
          Shape               Smallcaps
        EndFont
End


# Clear Address definition from lyxmacros
NoStyle Address

Style Address
        Category              FrontMatter
        Margin                Dynamic
        LatexType             Command
        InTitle               1
        LatexName             address
        ParSkip               0.4
        BottomSep             1.5
        ParSep                1.5
        Align                 Left
        AlignPossible         Block, Left, Right, Center
        LabelType             Static
        LabelString           "Address:"
        LabelSep              M
        LabelFont
          Shape               Italic
        EndFont
End


Style Right_Address
        Category              FrontMatter
End


Style Keywords
        CopyStyle             Abstract
        LatexName             keywords
        LabelString           "Key words:"
End


Style Subjectclass
        CopyStyle             Abstract
        LatexName             AMS
        LabelString           "AMS subject classifications:"
End


Style Bibliography
        Category              BackMatter
        Margin                First_Dynamic
        LatexType             Bib_Environment
        LatexName             thebibliography
        NextNoIndent          1
        LeftMargin            MM
        ParSkip               0.4
        ItemSep               0
        TopSep                0.7
        BottomSep             0.7
        ParSep                0.5
        Align                 Block
        AlignPossible         Block, Left
        LabelType             Bibliography
        LabelString           "References"
        LabelBottomSep        0.7
        Font
          Size                Small
        EndFont
        LabelFont
          Size                Normal
          Shape               Smallcaps
        EndFont
End

NoStyle                 Chapter
NoStyle                 Paragraph
NoStyle                 Subparagraph
NoStyle                 Chapter*
#NoStyle                Paragraph*
#NoStyle                Subparagraph*

NoStyle Verse    # Although mathematicians tend to be poets at times,
                 # we don't need this.


Style Section
        Align                 Center
        Font
          Series              Medium
          Shape               Smallcaps
          Size                Large
        EndFont
End


Style Subsection
        Font
          Series              Bold
          Size                Normal
        EndFont
End


Style Subsubsection
        Font
          Shape               Italic
          Size                Normal
        EndFont
End

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