similar problem myself originally, what i found is that i had used the software originally given to me with my sony camera to get some files off a 8gb memory stick pro duo card,it was onto a windows computer mind, then i recorded some more footage onto the card and went to final cut to log and transfer it off and i got the same invalid file structure rubbish, so i saved what was on the card onto the computer, then i formatted the card recorded under the same conditions and went back to final cut log and transfer and my new footage showed up.
Im guessing whatever software you originally use with your card/flash memory will change the file structure to its own end, and final cut doesnt seem to like this, so if your experiencing any problems save the material, format the card and try a test, it worked for me, hope this is useful.