Bro, I strongly suggest you run over to a CDRKing and get one of their 1Gb thumb drives, P300+ na lang ata. Low level installing firmware can be a very precarious process even for the hardware. A card reader and SD card combo still has a bit more points of failure than I'd be comfortable with.
Yesterday, I did a fsck (chkdsk on Windows) on our 2T drive which I suspected had a lot of errors already. I have it formatted in ext3 because I've been monkeying around the Mod Pack developed by the XTreamer user community. Well sure enough there were a lot of errors. Unplugging the XTreamer without powering down with the remote is not a good idea, though sometimes there is no choice. Also, I can't be sure but NTFS seems less prone to such problems but I'm not sure.