The first computer I used for my MAF swap did this. It would start ok cold, but if I drove it any and shut it off, it would not restart for a while afterwards. I checked and tested everything that I could though, I didn't just go buy a computer because I thought it was bad. I also couldn't get any diagnostic codes out of it. It could possibly be a bad TFI module as well, but unless it cuts off while running, I would doubt that it is the TFI..
I would start to suspect the ECM if you can't get any codes. There are a couple of places that will test it, and if it's bad will rebuild it. I don't have the links on my computer at school, but I think I still have them at home. I'll check this weekend.