Thanks for looking into it, Karel.
DAW: Logic 9.1.1, OS 10.5.8, VE Pro 5436 (AU)
Server: Kontakt 3.5 (VST), Windows 7 64bit (also tried XP64), VE Pro 5436
It doesn't always happen. But when it does happen, it happens on the same section repeatedly, about 80% of the time. Often moving a note away from the barline helps. The worst is when all notes are quantised to 1/4 notes. It seems to happen most often when there is a section with 4 intertwining legato string parts. I am using a private Kontakt strings library. I also tried removing all controller data from the tracks, but that doesn't help either. I am not getting the GUI hang, just note hangs, or non-playing notes. As mentioned the same patches work fine when VE Pro is in standalone mode.
I am ruling out the sleep mode explanation, as over a section some of the notes play, some don't, some hang, all over the course of a few seconds.