To make the sync between Pro Tools and Reason as tight as possible:

You may also want to experiment with the Latency Offset in reFuse:

Note that, due to the imprecise nature of triggering from MIDI Beat Clock, the latency will vary slightly from one pass to the next. The amount of variance can be kept to a minimum by keeping the Min Signal Vector set as low as possible.

Ultimately, to ensure correct timing, you may have to nudge the waveforms in Pro Tools by a few milliseconds once you have "printed" those tracks.

If, at this point, the problem is not solved, please contact us for further support.