It's probably just a patience thing. Try not to move to much when you're doing it. I had to do it about 4-5 times before I got a complete transfer. But it worked completey.
Thanks btw specialmias. The sad thing is that I did these exact steps last night and the night before using smallftp but I was too far from my AP so it was being gay about it. I had to literally sit right next my router when I did it but it worked. So thanks anyways though.
Also, have you tested yourself restoring the save yourself as I saw Noko's retail cart's save got erased when she tried but she's using a 3 in 1 EZ Flash.