Without seeing you run, I would guess that 1) your are holding tension in your ankles and 2) you are lifting your heel too high in the unicycle drill. Remember to keep your ankles loose and relaxed - as your heel comes up behind, your foot should just hang, and stay that loose through the whole cycle. Allow gravity to place it back down.
In first gear (warm up, slow) the wheel on the unicycle is very small. Your foot should come up to about midcalf. Trying to lift it too high while still fairly upright (only 1 inch of lean) will engage your hamstrings and cause tension.
Keep playing with it!
Certified Chi Running and Chi Walking Instructor