Same thing here, with Logic 9.1.8 and Mac OSX 10.6.8
First note missing on very first beat of loop. Not 100% of the time though but annoying enough.
At this point, since it seems to be an issue on different DAWs and different systems, it deninitely looks like it is something Arturia needs to fix.
Any news on some upcoming update ?
Update : This is also happening in Ableton...and actually more systematically and it loses sync on that 1st beat. Almost sounds like a late drummer who eventually catches up on the 2nd beat.