Is your iPad or another iOS device connected to the computer when this happens.
If so, give this a try.
With the iPad connected and selected in iTunes, go to the Summary section and turn off the checkmark that says to open iTunes when an iDevice is connected (paraphrased).
I also like to turn off the automatic sync. You do this in the Devices tab of the iTunes Preferences (found in the iTunes menu). If it is checked, then the previous setting will be grayed out so that you can not change it.
Not that thees settings should cause the problem you describe, but if for some reason Windows keeps seeing the iPad replugging itself in (maybe a poor USB connection) then it could cause the problem.