HUH? Filled the tranny with tranny fluid through the radiator hoses???? Are you SERIOUS!?! I mean, are you SURE you saw them pumping ATF fluid through one of the radiator hoses?
Ok, let's step back here... did they actually flush the tranny fluid out? If so, did you see them? If so, did you see where they hooked up the flushing machine? Was it to the tranny or the radiator? Did you have your antifreeze replaced at this shop at the same time?
Check the antifreeze (take off the radiator cap when the engine is cold and look for dark-colored fluid), also check the radiator coolant overflow tank and see if the fluid is darker and thicker than normal.
I would also get under the VX, after it's been running for a couple minutes, loosen the overfill screw and see if ATF comes billowing out. You may need to add a bit more in if needed.
Jeez... let's HOPE they didn't add ATF to your radiator!