Stevie - Yeah, the SQ1 has some strange behaviors, but it's still great to use for CV conversion and CV send. You can do stuff like using an LFO (or a happy chain of LFO's) in your DAW to control filters and pitch on analogue gear etc. Great for sound effects!
Look at "Preferences" and the tab that says "Sync" in Reason ;-) Then check the "MIDI clock sync" and set the "Input" and "Output". Then be sure that the box "Send MIDI clock while sequencer is stopped" is uncheck...........and you should be good to go :-)