I encountered this problem awhile back with the regular arpeggiator, and it's also happening with the (sync) arpeggiator. I was using K5 for years and never had these problems.
Over on VI forum, EvilDragon suggested the script editor being open was the problem but even with that closed I get either no playback or, most often, notes that stick from chord to chord and never shut off on stop.
I noticed a lot of posts about this problem here on the NI forum and they're all closed with no solution posted. (No, this is not a latch problem)