Well, with a bit of fixing I was able to move the three projects back to Vegas Pro 8 to render them out and not have the flickering thanks to the export and import XML script Sony includes.
I'm surprised I never realized it before, but that is a pretty impressive problem to be introduced into the new version that wasn't there before. I hope I'm not the first one to put in a support ticket on it, (e.g. - I hope it's fixed in the a release or I will have little to no use for 9 for some time).