During installation you're legacy installer has registered the DLLs in the registry, MSI wants you to use the internal COM registration (right mouse button on a DLL/EXE file within a component that has been given a "_COM" suffix, you should have eaither "extract COM data" or "refresh COM data".
If the COM data was extracted sucessfuly, you should have a few entries under ComponentName/Advanced/COM Data
You will notice that a lot of the registry entries for the same component will be under HKCR\Class or TypeLib (third one escapes my memory), the registry entries can usually be deleted as they are duplicates of the COM registration.
Hope this makes some kind of sense 🙂