Hmm, that's interesting. Maybe some indi in the repo is acting up.
I've had this 2 times, first time I had 2 Pro's installed but they each used the same indi folder. I deleted one Pro and issue disappeared.
The second time happened with 2 indis which were badly formatted by me, I took them out and everything worked. Later I fixed them and everything worked again.
If you want my advice, clean the library first. Then, move all custom indis to a separate folder. Then, take half of those indis and put them back into respective FSB folder, start and then restart. If everything works, clean the library and indi folder and repeat by adding the other half of indis into FSB. Check if it works. If one group of indis work and other do not, then you have a bad apple in non-working indi group. You have to repeat the library cleaning-division-testing cycle until you have the bad apple left.
That's all I can say at the moment.