You need to edit the xml file that provides the markup definitions. Depending on the distro, the file is
/usr/share/apps/katepart/syntax/latex.xml
~/.kde4/share/apps/katepart/syntax/latex.xml
/opt/share/apps/katepart/syntax/latex.xml
/usr/share/kde4/apps/katepart/syntax/latex.xml
You then need to add your environment name to
<!-- filter the environment name and check the type -->
<context name="BeginEnvironment" attribute="Environment" lineEndContext="#stay">
...
<RegExpr String="(equation|displaymath|eqnarray|subeqnarray|math|multline|gather|align|flalign|IEEEeqnarray|IEEEeqnarraybox|smallmatrix|pmatrix|bmatrix|Bmatrix|vmatrix|Vmatrix)" attribute="Environment" context="MathEnv"/>
...
</context>
and also to
<!-- end of math environment -->
<context name="MathFindEnd" attribute="Normal Text" lineEndContext="#pop" fallthrough="true" fallthroughContext="#pop">
...
<RegExpr String="(equation|displaymath|eqnarray|subeqnarray|math|multline|gather|align|flalign|alignat|xalignat|xxalignat|IEEEeqnarray|IEEEeqnarraybox|smallmatrix|pmatrix|bmatrix|Bmatrix|vmatrix|Vmatrix)\*?" attribute="Environment" context="#stay"/>
...
</context>
~/.kde4/share/apps/katepart/syntax/latex.xmland edit that version – StrongBad Feb 12 '13 at 16:04