I wouldn't take the outlook that every running shoe (something with a larger heel) would lead to soreness. Running shoes are made for different pronation and suppination ( good article here: http://www.thestretchinghandbook.com/archives/pronation-supination.php ) Also, different brands of shoes are going to treat your feet differently.
Another big thing to consider is the distance your running. Just make sure you are not overdoing anything at all, being it running with no support or running in running shoes.
If you haven't read "Born to Run" I would highly recommend it.
Hope that helps