My '05 OBXT had the same problem, and it turned out to be a good deal for me. The original owner (down in SF, CA) ended up getting SOA to buy it back as a lemon. After they bought it back, the factory came out with the fix to the computer programming.
My friend who works for SOA helped me get the car after they had repaired it. I ended up getting the car (Limited Ed., MT, 28K miles) for under $15K. Of course it has a branded title since it was a lemon law buyback, but if I keep this like I kept my last 2 ('76 4WD, 351K miles; '82 GL 4WD, 327K when it was totaled), the brand won't affect value at all.