When I would load sample libraries and convert them to patch phrases, I was getting directory errors when I would save them. I formatted and reformatted. Both compact flash and internal hard disk gave me the same errors. I was able to save them to internal memory (5mb worth).
In the end I called Akai and we tried renaming the samples with only two character names. This was the issue for me. For some reason the loop samples on the cd had too long of a name for the mpc to save it without erroring out.
I forgot to mention that a hyphen was in some of the names. That seemed to really screw things up. Between removing that and shaving a couple characters, things improved.