Intermittently dropping in to record on playback

[tinfoil]

Got an interesting problem, running protools 6.4.1. The protools is driving a Merging VCube (video playback) machine via 9-pin (Machine Control), and when you have tracks armed and "play" the tools with it in quickpunch, it sometimes punches in to record and sometimes doesn't. This also happens when tools is off-line and has only started happening recently.
It's possible to tell if it's about to drop in, because when you hit play, the record button lights, then goes out until the video is locked up, at which point it then punches in.
I'm positive that it is just a tools issue as the tools is the master but I thought I would give you the overall situation.
Any help would be greatly appreciated.