Could you please let us know if the article Jennifer Jiang referrenced above helped you resolve this issue. By the way, the article refers to ICProjConvert120.exe which resides in C:\Program Files (x86)\Common Files\Intel\shared files\ia32\Bin folder for a VS2008 installation.
You said converting Microsoft projects to x64 projects in VS2008 worked fine for you. So, if the information in the above referrenced article did not help, rather than converting your Microsoft x64 project to Intel project directly in VS2010, you could try converting it to Intel project in VS2008 IDE, close VS2008, and then load the Intel converted project in VS2010. At this point, the project should have already been converted and loaded as an Intel project in VS2010. Please let us know if this works.
If none of the above works, please send us one of the empty Cuda x64 projects that you said you experimented with in your earlier comminucation so we can reproduce this problem and root cause the problem.