I had some material on my memory stick when I went to dump Dissidia (a new copy) so I didn't have enough room so it filled it up and told me to insert a new memory card, removed the personal material put it back into the psp and finished the dump. Had two parts, used the provided bat to combine them /b copy like we use here but the checksums didn't match the db, thought I might have another release anyways deleted it off memory card and dumped it again fully this time and that dump matches the db.
So there might be a bug having pspfiler separate into parts. Either it's that feature itself or because I had the first part still on it, messed up the dump. I am not sure.
When I am done dumping new games I will go back and test it by removing the first part1 and see if I get the same results.
EDIT: Looking at the two sizes they are different, the one with parts is 1645182976 to the fully dump one of 1646657536, so something is wrong with that way, I will put the same personal material on and retest it with taking the first part off the memory stick before dumping the second.
EDIT: Completed my test, pspfiler has a problem with dumping parts. The new part dump matches the first one. Which means if a dumper has to dump that way and dumps the game twice it will match but be incorrect. I hope it's just my setup, I have 5.50 Prometheus V4 CFW and is using PSP Filer Ver.6.6