I have the exact same issue here, using Vienna Ensemble (32bit) as the host (linked to Logic Pro) - Mac Pro 12 core, 32GB Ram, 10.6.8.
All other Arturia synths sync to MIDI clock fine, but the arp on the SEM periodically starts to speed up. When it happens I have to remove the synth completely and re-instantiate it, then it's generally fine for a while.
Hard to give you a recipe to reproduce, but it happens fairly regularly here. In my case it always goes early/fast - never late or slow. The fact that other Arturia synths don't do it seems to suggest it's definitely an issue specific to this synth.