Long story short, it appears the A/D converters are sampling too fast and the latest firmware is not processing the AD interrupts fast enough.

The AD interrupts are currently coded to interrupt the CPU 4 times at 4us intervals for the 4 A/D inputs (16us in total). After the latest additions, the firmware was not able to process AD1 within 4us of requesting the AD cycle and was dropping AD2.

I've changed the 4us to 8us (32us total) and the firmware works correctly again.

Regards
Paul