If VS/msbuild really depends on the registry setting, you may need to change the registry setting within the build (and change back after building VS2012 solutions).
Another possibility is to specify the VS2012 environment by running vcvars32.bat/vsvars32.bat beforehand (see the Advanced tab,
Command to run before main command field):
http://www.kinook.com/VisBuildPro/Ma...dvancedtab.htm
Also see
http://www.kinook.com/Forum/showthread.php?t=4500