I had a problem similar to this before. Or, at least I think it's similar to this, judging from your description...
Personally, I renamed all of the .girls to .girlsx files and deleted all duplicates using the character editor tool. Make sure you have a .girlsx.bak file as well, of course. Deleting those isn't a good idea at all. Oh, and I loaded every single pack into the editor tool, THEN deleted duplicates.
Do the same for random girls.
When I did it, having both types of files didn't work out well.
Make sure you don't check the gallery for 'blank' girls or it crashes.
Make sure you have pictures for every girl that you've added.
It's been a while, but it sounds similar.