It seems that the manifest step is not running due to a path issue (??), but I am not sure.
It is easily reproducable, just need an MFC App from the MSVC wizard, and build the solution file in teamcity.
Note that building the solution file using cmd line and msbuild from the same directory in the build server works fine.
Log file is attached.
C:\Program : general error c1010070: Failed to load and parse the manifest.
Is that a bug that I should report or am I missing something ?