Hi there,
As this thread is still active, I thought I'd respond because of some miracle last night, I managed to fix this issue. It is more of a technical fix, but essentially the resource.cfg and the fact that I had my CC package files in sub folders was the error in my case. (Even though I'd been using subfodlers for a while, after one crash I guess my game decided to just stop allowing that. Anywho...)
So, after doing some research I saw that the Mods folder only allows for one subfolder (still unsure if this is true for all cases..), and so I edited the resource.cfg to expand that limit. First I created a backup of the resource.cfg file. Then edited the original resource.cfg file with a text editor simply to:
Priority 500
PackedFile *.package
PackedFile */*.package
PackedFile */*/*.package
PackedFile */*/*/*.package
PackedFile */*/*/*/*.package
PackedFile */*/*/*/*/*.package
Then I saved it. And opened my game - voila. After months of trying different things, all my CC was there. Thought I would share because this seems a bit of a lesser shared fix amongst advice I have seen through my searches.
BR,
Carly