This is a side-effect of the original problem you had, the COM server wasn't getting registered properly. When you Isolated
option to true, the build system auto-generates the required manifest entries for you. But the content of the manifest needs to come from somewhere, it uses the registry keys. Since they are not there, it can't generate the manifest.
You can write the manifest yourself but that requires enough insight in what the manifest should look like. With very high odds of making mistakes, the incantations are quite obscure. So avoid that, you just need to get the COM server registered to get ahead. Just on your build machine, it doesn't have to be registered on the client's machine since it will use the manifest.
You mentioned a 64-bit COM server, that's another possible failure mode. The build system is still 32-bit so you'll have high odds that it looks at the wrong keys. HKLM\Software\Wow6432Node instead of HKLM\Software. Battle that problem by building both flavors of the COM server. Beware of having the same kind of problem when you use Regsvr32.exe yourself, there are two of them. The one in c:\windows\syswow64 should be used to register the 32-bit version of the server, the one in c:\windows\system32 for the 64-bit version.