That's possible, but I wouldn't count on an upgrade to solve it. We ran CS3 on Vista for some time and I don't remember experiencing longer conforming/indexing.
Quicktime DVC Pro HD could be the issue. Especially the QT part, Premiere has had a lot of issues with anything Quicktime for the past 2 years, CS4 was not help...
I know that you don't have many options for encoding, but I would be tempted to try something else, at least a native AJA codec to start and see if that helps.
Vince Becquiot
Kaptis Studios
San Francisco - Bay Area