Hi Ryan,
Are you able to confirm this behavior by using a simple project that will have no other variables, just the Wait on IRQ and Acknowledge Interrupt Invoke Node? I would like to confirm that this is not due to faulty hardware or something else in your program.
When you do this, can you post a quick picture of the code? If you are able to still get the error that way, it might be easier to attempt to reproduce.
I misspoke about the RT not being able to assert an interrupt on the FPGA. You cannot write your own interrupt service routine. If you have been successful in the past, it might be possible but it is not recommended.
Nick