Under GLOBAL > MIDI, there's a setting called ARP BEAT SYNC. Are you using that? Also, are you running the latest O.S.? 1.0.3.45?
If you set ARP BEAT SYNC to QUANTIZE, it locks in with incoming clock signal. I often use the Pro 3, set to follow the TR8S clock and it stays in time perfectly. For complex phrases with lots of changes, the arp quantize is very helpful for keeping in time. I use it in most cases, unless I'm trying to establish a specific timed groove with drums.
I do wish there was a manual timing offset capability for the arp/seq, where you could adjust the quantization sync point forward or backward by small amount... It's nice to be able to have the quantization/lock to stay in time, but have the ability to adjust the feel of the groove by slightly moving the beats in juxtaposition with drums or other sequenced instruments.