Let me just complement with something we did for Lua for Windows. The LuaBinaries DLL today do not have the manifests embedded. And we had some minor problems that were best solved if they had.
So I build a custom DLL for Lua for Windows to have some feedback on this issue. But the LuaBinaries DLLs are not dynamically loaded, so it is not the same problem reported by Ryan.
I was just ready to release the next IUP version including the manifests. I think it is a good idea that modules developed with VC8/VC9 have their manifests embedded. This explicitly says to the system what RTL DLL you are using.
This problem needs to be further investigated. So far I understood that the problem occurs only when using the "lua.exe" executable in an environment that does not have the mscvr80.dll installed on the Windows repository, right?