will try to reproduce when i get back at home on saturday ..... but when you hit play then stop then record , is it happening ...?
what is strange is that it contuniues playback after you stop ....do you have a count in in the record option in sonar metronome option , i don't see it well .....as i don't have this might be why i never seen it on my set up ;)
EDIT : i just rewtched the video .....change the countdown to 2 bars just to see if it works ...also have you tried not satrting at 1 mesure but make project construction (looping) from let's say the 4 th bars ..?