Another reason could be if a game has a file larger than 4gb and is copied to an external harddrive the large file is split up for the game to run it needs to be copied over to the ps3 internal hdd to merge the split file together again. multiMAN takes care of this on the fly also.
Long story short, try using multiMAN and if a game doesn't work try it on the internal hdd.
And you didn't think maybe that was the problem? I use deanrr's multiMAN backup manager and don't have this problem because it patches the sfo on the fly which fixes alot of those black screen errors.