Trumany, Yes. One of the boards smelled like it was burning, so I opened the heat plate and noticed that U117 was completely damaged.
I just noticed that the power input for VIN_PWR_BAD# is from 0-5V. We have had that connected to 12V for over a year and that has worked fine until now. There must have been a change in the voltage range of that buffer chip(U117), which is now causing it to get damaged. I have been testing with VIN_PWR_BAD# tied to a 5V line and it has been working so far. Thanks for the help!