If you are quite sure the splitted files were in a different folder... Can't imagine what the cause for this bug could possibly be.
Are you really sure they were in USRDIR? The program takes the path of a BIG file and just adds the extension to it when saving small files. For example, it knows the BIG file is in ...path/bla/BIG.fl - then it adds .66600 or .66601 and so on to it whithout considering the directory. so out comes: ...path/bla/BIG.fl.66600 and ...path/bla/BIG.fl.66601 and so on. Because it already knows where the BIG file is, right?