The copy issue of files saying 94gigs occurs from my experience on files that will not natively playback on my PS3 anyway. It appears to be some sort of reading error between the PS3 and computer. You should still be able to transcode the files with no issues, use the file in #--Transcode--# folder and see if it still has issues on playback.
Also what kind of file types were they, saw you had 1.03exe and that worked but would like to see what the problem was anyway.
Core2Duo E8400 (@ 3.0), 8gigs of Mushkin, Vista Home Premium SP2 64bit, 2.5 TB of Space, Wired to Linksys WRT54G wired to 80GB MGS4 PS3 on Sharp 32" 720p LCD TV