Using a custom board with MK02FN64VLH10 controller, KSDK 1.3, PE 10.6.
I have set up the ADC in the 16 bit differential mode, trigger the ADC from a PIT interrupt (every 62uS), The Interrupt code is shown below: I take samples and stores them in arrays, as long as the arrays are not full. While samples are being taken and stored in 1 array, I am taking an FFT on the filled array. This works fine the vast majority of the time...
Problem is that after some time between 1 and 10 minutes of continuous good operation, the program gets stuck in the
ADC16_HAL_GetChnConvCompletedFlag
routine and seems to stay there. The interrupt continues to occur, so code is running OK. Since the buffers are now full, it just skips the ADC conversion and returns right back to ADC16_HAL_GetChnConvCompletedFlag waiting for a conversion to complete...I assume.
Does anyone see anything wrong with the above code or the implementation of starting a conversion, waiting for completion, and getting the value? I tried to manually wait for the COCO bit to set, and that works OK, but has the same problem...
Any help would be greatly appreciated!

Thank you,