Hi Denise,
I started my extension project with Visual Studio 2008 to use plugin that creates required projects (Project Centre, Win and Win Mobile). I compiled and copied DLLs to necessary folders. I could see and use the extension in MPC.
I then opened the same project in VS2012, changed the target framework to 4.5 and recompiled, no other changes. This time MPC could not see the extension. When I targeted the framework back to 3.5 still in VS2012, surely the extension started appearing in MPC extension list. So my guess is somewhere MPC checks the dotnet framework version of the dll found in the C:\ProgramData\ESRI\MobileProjectCenter\Extensions folder, though I am not sure why.
Cheers,
Vish