I have had similar issues trying to my car updated using the older UPD1004 file. Car simply won't recognize the software update. My dealer was also unable to solve this. I have tried several different USB sticks, reformatted using a Mac and a PC etc but no luck. The dealer spoke with the BMW engineer and I am getting a full software update next week to see if this will solve the issue. Good luck!
2011 Space Grey E90 M3, DCT, Comp. Pkg.
1997 Z3 2.8, Artic Silver, Tanin Red interior, MT
1974 2002tii, Inka, MT