Similar issue, but mine is happening during playback.
The arpeggiator is introducing delay to a point where the midi notes sound like they're not on the grid.
What's bizarre is that there are no issues when I play an individual clip in my arrangement, but as soon as I play the full track through, my pluck has a very noticeable delay.
I switched to using Ableton's stock arpeggiator with the same settings--resolved the issue immediately.
Troubleshooting this was a pain. I thought my patch had attack on it somewhere or a free running LFO