Yeah, HIDs don't like to be flashed. (Keep this in mind when using the high-beams, as the stock configuration turns the fogs off when the high-beams are activated*).
To keep the fogs from flashing when you use the key fob, just flip the fog switch to the "OFF" position. Voila.
*There is a write-up somewhere that shows how you can alter the wiring to allow for all 6 lights (fogs, lows & highs) to stay on at the same time. Granted, it's against the law to have 6 lights on at the same time (hence the factory settings), but this will eliminate the on/off of the fogs if you have to flash your high beams.
*edit* here is that write-up I mentioned: http://www.ls1tech.com/forums/appear...same-time.html