Hi Nick,
I understand your problem description, but not clear of certain points:
I assume, you are pointing to SIC_ISR bit of MDMA interrupt in problemactic case. I mean, sometimes processor enters in MDMA interrupt handler, but you see corresponding SIC_ISR bit is not set. Do you see this problem for MDMA interrupt only or for any other interrupt?
how you have mapped to the interrupts? I mean, what other peripherals shares the same IVG level with MDMA interrupt?
You mentioned that , 'Inside the interrupt handler, you read the SIC_ISR register and then check each peripheral under that SIC to determine the source' and 'if you check each peripheral and skip checking the SIC_ISR register everything works every time'. Can you post the code to explain these points?
Are you keeping default mapping of interrupts to IVG levels? If yes, is there any reason in doing so? I mean, if there are few interrupts in your system, you can map those to different IVG levels, so that checking for interrupt cause may not be needed.
Please get back with these details to understand the problem in better way.
-Prashant