I have a TeamCity install on x32 Server2008 windows machine. I\'ve run the .net 4.5 web install. I\'ve also copied over the files from my x64 machine based on this article
I had this problem on my secondary build agent.
I had copied the MSBuild folder from the primary build agent pc to the secondary build agent pc (like I did with some Visual Studio files as described here: MSBuild in TeamCity of Visual Studio 2012 solution), rather than installing MSBuild.
It seems, however, that the TeamCity agent services checks the registry for MSBuild entries when it starts up (it does not seem to do this with the Visual Studio files i mention above). Since I had simply copied the files from the other pc, no MSBuild entry for v. 12.0 existed, so TeamCity did not discover the MSBuild files even though they were present in the Program Files (x86)\MSBuild folder.
When I installed the Microsoft Build Tools from the link above http://www.microsoft.com/en-us/download/details.aspx?id=40760 TeamCity found the v. 12.0 entry in the registry and the agent was able to build the same projects as the primary agent.
Remember to restart the TeamCity agent service after installing MS Build Tools.