Just to check -- do you have the same input enabled for MIDI control messages as well as for MTC synchronization?
There are two separate systems in play -- the MTC synchronization, and the MMC control going through the "MIDI control messages" side.
The MMC messages, when stopped, are treated similar to repositioning the cursor via control surface, which has some logic to determine whether or not a scrub is desired (how recently you previously scrubbed, how far there is to go, etc). You can change whether scrubbing is used at all in Prefs/Playback (near the bottom).
If you're seeing something inconsistent with that, maybe send me a .mid file of the actual messages being sent, plus details on how the device is opened/etc, and I'll take a look
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