I got similar problems, and can not find out the reason.
I migrated My customized ArcMap dlls from 9.3.1 to 10, I'm using VB.net 2010, created Setup MSIs, using ESRIRegAsm in .vbproj. Everything is working as expected.
However, when I recompiled my dlls and compiled MSIs, and installed MSIs on Windows 7 enterprise PC, The installation is successfully completed. When I open ArcMap 10.1, go custom-->Command-->Categories, I can not find the Category which my dlls should belong to. When I manually ESRIRegAsm my dlls, I can find them under My category. Do I have to use Command ESRIRegAsm to register dlls?