Did you try to return to previous firmware version? What's the previous version and current version?
I'm not aware of any way to return to previous versions, SCT only supports the automatic updates. Maybe they save them somewhere and could manually send it to me, not sure. The problem is that I don't know what FW I was using when the tuner was
I just downloaded the latest FW (1.2.145-3015, released 10/08), which worked, then attempted to download the latest Tune Revision (2.041 - Full Version, released 10/08), which failed. I have not yet tried to re-tune the car, I don't feel comfortable doing so until the Tune Revision "takes". This is using the latest Device Update Software (184.108.40.206, released 10/11), btw.
Moral of the story: if your SCT tuner works, DON'T MESS WITH IT.
Mine: 2002 Focus SVT: 142k, Sonic Blue, #1654, All Options
Mods: Tom's Tune, Borla, HFC, STS, Painted Machs, Euro Grill, FRPP Springs
Hers: 2010 Focus SES: 67k, Ebony, Auto, Moon and Tune