What I am doing to resolve it is a multitude of things. First, run sprinter as Administrator (if you can disable UAC, do it). Second, under the application settings for your test, uncheck the "Start the application when the run begins". Then uncheck any uneeded "Technologies". If you are testing a web page, just choose Web. Then run your test and manually launch IE 9 AS ADMINISTRATOR. Also add exceptions to your anti-virus for the Sprinter.exe, sprinter Agent.exe and iexplore.exe. We also increased RAM on all our test workstations from 4GB to 8GB and that seems to help ALOT. Add the websites you are testing in IE 9 "Trusted Sites" and consider lowering the security settings.
We also see aproblem with dual monitors and multiple IE 9 windows open before the test starts. Sometimes we get recordings of the other IE 9 window when working in another, but the capture is of the first monitor. Very very strange.
We are still working through issues. I will post back as I get more.