ambrop7: The 10u caps were originally on the Mega (5V), so we may need to change their values for decent readings on the Due (3.3V).
That said, it should be noted that RAMBo has removed those 10u caps completely, so maybe it might be worth removing them and seeing how that goes?
Things that might be related:
1. Induced voltages in the thermistor cables from the hot end cables.
2. A high resistance path from a hot end pin to a thermistor pin.
Each of these may not change the voltages by much, but they might add up with the 3.3V rail change to be a noticeable difference.
That said, it should be noted that RAMBo has removed those 10u caps completely, so maybe it might be worth removing them and seeing how that goes?
Things that might be related:
1. Induced voltages in the thermistor cables from the hot end cables.
2. A high resistance path from a hot end pin to a thermistor pin.
Each of these may not change the voltages by much, but they might add up with the 3.3V rail change to be a noticeable difference.