I've been having the same issue with mine for the past few months, but I can't get custom tunes on at all, or perhaps I'm not trying enough times. I haven't gotten around to calling SCT yet. I have an SCT SF3 tuner, and the most recent firmware. (It worked before on a previous FW version, of course.) Not sure if this is related or not, but I'm also unable to download the most recent Tune Revision to the tuner via the automatic updater. I'll post a solution if I ever get it figured out.
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