Hi Sean,
I don't see this behavior in AQtime Pro 7.30 x64 (the latest version) on Windows Vista using the Performance profiler. Perhaps, it's caused by specific operating system, compiler or profiler settings that you are using, but the details in your post are not enough to know this for sure.
I'd recommend that you go through the
AQtime Troubleshooter for some advice solving the problem. Even if the troubleshooter doesn't help figure out the problem, it'll help you collect more background info and submit a support ticket for further technical assistance.