Yeah, syncing the arp to a DAW (Pro Tools beat clock in my case) only works when the rev2 receives a "MIDI start" message, which Pro Tools only sends from the very beginning of its timeline (bar 1, beat 1). If you start playback from anywhere else in the timeline, Pro Tools (and many other DAWs) send a "MIDI continue" message, which the rev2 ignores and thus the arp will be out of sync, even though it's at the correct tempo. Sequential support has recently confirmed this with me. Pretty sure this goes for the sequencer and LFOs as well - anything that can be clock synced. It's a drag and I'm looking for a work around.
Support suggested sending a pulse to the rev2's Seq jack and setting the Seq jack global to the trigger setting. I've yet to try this again, but I've been annoyed by this problem for a long time and a while back tried something like this. The problem was that, while it worked, I couldn't change the time division of the arp on the rev2. I'll give it another shot one of these nights.