Who said hes using a midi clock and not manually syncing ?
If you scroll back a bit you will see a video of Deadmau bitching about syncing laptops together its an issue thats not yet resolved. As much as i dont like Deadmau the dude does know his stuff, so if you wont take my word for it, take his word for it ;) Midi clock sux the big one.
Basicly the best and most reliable way of getting these programs working with one another is the old fashioned way of syncing manually - its when there is tempo changes that things get a bit messy, i mentioned a half arsed work around earlier in this thread that will keep the tracks in time better than a midi clock is capable of (but still not perfect).
I wish i could give you guys better answers, but there just isnt fairytale answers.