My car does the exact same thing. I took it to the place where the transmission was rebuilt several times because of this. It seems to start blinking when I am driving around for a while, especially in top gear. After the light starts blinking, it shifts really hard, eventually going back to normal. The transmission place said that they didnt know what was wrong with it, and when they ran the diagnostic, the only thing that came up was my EGR (which I still havent replaced) SO I don't know. I know that this car has 125,000 miles on it, and I am about halfway saved for my new car. I just hope it lasts until then.

1996 Contour GL AT, 2.5 V6 No mods, rollin on 14's with hubcaps, 116,000 miles, and still havent been beaten by a ricer.