Not having it done professionally is usually the problem. Since I am "in the market" for a WRX, I've done a crap load of research on tuning and warranty problems. 80% of the "bad situations" that I have heard of are due to amateur/DIY tuners. I have also read about several instances where there is a tune professionally done and if the problem with the car is unrelated to the tune, the dealer doesn't care. I have also heard of a few instances where the pro tune company "untunes" and is undetected. At the other end of the spectrum, the DIY tunes usually cannot properly untune.
That is just the overall summation of what I have read so far. Set me straight if I am wrong.