Hi,
> [...] there is a pretty significant time for the "Main" module. Is there a way to only have it track when the application is active?
I am not sure if this is possible because there is no definition (or the way to determine) of what is the active application. From the profiler's point of view, the code is called and thus it must be counted. Profiler has no idea of whether the called code just checked the keyboard queue or did some intensive background calculations. On the other hand, you may be interested exactly in verification of the keyboard polling code, so no reason to exclude it from profiling by default.
> I am just trying to get a better handle on the product.
I would recommend to go through the http://support.smartbear.com/viewarticle/54562/ help section and, maybe, some related ones. AQtime has extensive help documentation that provides a lot of information and really worth reading. I think that you should be able to get what you need with the help of different Time columns (Time, Time With Children, etc.). Note, that not all of them might be displayed by default.
Also I would recommend to watch the videos (http://support.smartbear.com/screencasts/aqtime/).
Hope, this will help.
