MSI and MFC

Ok, folks, here's the problem:

I migrated from Visual C++ 6.0 to Visual Studio .NET and have been writing my new software in C#. Unfortunately, I still have to maintain legacy MFC code. That's not so bad; the problem is that I'm having difficulty building deployment projects for my MFC apps from within Visual Studio .NET. ActiveX controls don't get included, the system can't register them, and the app is squarely buried in DLLHell.

Has anyone had an issue similar to this? Does MSI not play nicely with MFC?

Thanks in advance for any help or advice you all can offer.