I'm starting a thread that's attempting to be a bit more clear. I saw a couple others... I just updated to PT11.1.0 OSX10.8.5
I've seen people post this issue with Superior Drummer, Addictive Drums, I did my tests with Kontakt 5 and Battery 4.
Toneshed did his tests with Aux tracks, mine Instrument. So it's not track type specific. Any instrument/sound routed to a multi out to a separate track with plugins WILL NOT be in time.
Video that Toneshed made:
https://www.youtube.com/watch?v=U3wGdbKhJyc
This issue becomes even more pronounced with high delay plugins. Waves UltraPitch Shift the delay was almost a quarter note. This issue effects everyone making music with multi output VIs. As a composer this makes PT11 useless.