Well, unfortunately you can not blame Apple (QuickTime) for this problem, guys. BRIO Technologies is a Microsoft Business Partner and their plug-ins do the exact same thing, which is nothing. I have noticed that the similiar bond between BRIO's plug-in and QuickTime is that they both use JavaScript to launch the plug-in.
I had one of my developers create and Active-X plug-in to test the problem to see if it was just Active-X plug-ins (since ever Java plug-in has worked for my team). What we found was that if we called the Active-X directly it ran fine, if we launched it through JavaScript, we had the exact same problem the QuickTime and BRIO have... Unfortunately I do not have a solution, but maybe this will spark something for someone.