can you get a picture of the atmel?
the atmels are much more approachable to reprogram, so there might be a solution here. you should definitely bust out your old scope and figure it out.
is there a crystal for the atmel? a ceramic resonator? if they are running the atmel off its internal RC timer, that can easily have a 10% drift, and would account for the error. that is fixable by recalibrating the internal RC timer, or putting a crystal on it. but both of those solutions require modifying the micro.
here is my guess as to how it works:
1. the atmel does all the dirty work - measures the tap rate, samples the knobs/buttons, makes leds blink, and writes data to the screen
2. the DSP does the DSP - it gets passed variables from the atmel which tells it what the current control settings are, and it just chunks through the data.
so what is probably happening, is that the atmel samples the footswitch for the delay time, and has its own internal timer it uses to blink the LED. so the LED matches what you tapped in. it also displays this value on the screen, but this is done in aboslute terms, which shows the wrong value because the atmel clock is off. it then sends this off value to the DSP, and the audio gets processed wrong. if you fix the clock on the atmel, you fix the problem.