We figured it out, at least the 720×720 capture issue.
We installed Quicktime on the PC using the standalone installer from Apple downloads. We went back and installed the standard iTunesSetup.exe version from Quicktime.com and now it works. I really didn’t want to have to install iTunes as well but looks like the only solution.
We’ve confirmed this by uninstalling and reinstalling from the stand alone version and it breaks it again.
We have some other problems as well though, and these showed up in Machina too.
We are doing long captures. We’ve seen problems where the video will all of sudden go white and the audio will get distorted. It has happened on multiple captures using 2.0 of the drivers usually an hour or so into the Quicktime.