User defined props for MSBuild stored in %LOCALAPPDATA%\Microsoft\MSBuild\v4.0 are shared by all PlatformToolset configurations (v90, v100, v110..). This can be a problem when you want toolset specific setting, especially for LibraryPath.
Use Condition attibute like the following:
<LibraryPath Condition="'$(PlatformToolset)'=='v90'">
$(LibraryPath);/path/to/vc9/specific/libs
</LibraryPath>
<LibraryPath Condition="'$(PlatformToolset)'=='v100'">