First off, what size are you running that the shop doesn't have it??
Second. The pressure of an inflated tire will help hold the rim true somewhat. This is why they suggest that you let the air out of your tire before you true the wheel. That being said, this effect is not enough to correct for the wobble you are describing.
I have never heard of a blowout alone causing a wheel to go out of true. If you have an inexpensive single walled rim, it is possible that the flat tire allowed the rim to take a hit that could cause this. Otherwise you have a mystery. Are all the spokes okay?