SOLVED:Arduino Due Delay Effect - Noisy playback *only* with variable delay time

But the noise goes away (even when still reading the pot) at the max and min settings of the pot.

In which case have you tried putting a serese resistor of about 20R between the top of the pot and +5V. Then put a 47uF capacitor from top to bottom of the pot. Finally put a 1uF capacitor from the wiper to ground. This would reduce the electrical noise from the pot and give a more stable reading.

Have you tested how much noise you have? Just read the pot and print it out, what sort of variations do you see? You could also try a running average on the readings from the pot. Any jitter on the delay will cause noise due to an inconsistent sample rate.