So here's the setup.
Instant Track Mute On/Off... all other s
Track 1 - Kick/Snare/Hats (at 1/8th notes)
Track 2 - Hats (at 1/16th notes)
If you Track Mute Track 2, and have Instant Track Mute On, then you get these shortened high hat notes.
As you can see here, turning Instant Track Mute off allows the high hats to play properly, but with Instant Track Mute on, they play chopped. That's the only setting change.
Guess it is time to live without Instant Track Mute :D