Im not sure exactly what causes this but when triggering a frame motor with a timer regular the minimum interval you can use is 0.8 seconds. As i'm sure you know this results in a smooth continuous movement.
If you attempt to do the same thing with a timer in an ic gate the motor misses every second pulse. Its as if the gate timer is running faster or is somehow out of sync in some way.

This is outdated now, due to a pending rewrite: #1616