40% of images missing when shooting tethered

I'm testing LR3 as a possible alternative to C1, and I like what I see so far.  However, there is one big problem.
We're shooting with a 5d Mk2, and used LR3.  After waiting a while for a low-pressure shoot to test LR3 with, we got it running and tethered the camera.  All was good at this point, but during the shoot there seemed to be less frames coming in than were shot. 
At the end of the shoot the connection dropped, so we shot the last 30 frames to card.  I decided to check the whole shoot by uploading all cards into a seperate folder from the tethered folder - turns out there were 230 more frames in the card folder than in the tether folder.  And it's definietly frames - not sidecars or anything else that's giving me the discrepancy.
Has anyone else come across this?  I'm making a call on LR3 vs C1v5, and right now LR3 is my choice bar this huge issue.
Any thoughts?

Thanks Sean - appreciate the words of wisdom.  There's a pretty good chance I wasn't paying attention to the tether pop-up while shooting, so the cable may have come loose.  That said, it must be happening a lot and in small sections, because it's a few frames every now and then that are missing. 
Definietly gives me option #1 to troubleshoot.
Cheers,
Kev

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