It could be a setting to prevent stealing focus, or an always on top setting with another utility has been enabled.
It could also be a problem with your video card not updating correctly.
Does it only happen with IE?
Do you have any other browsers such as firefox or opera?
Does it happen in either of these?
http://www.opera.com/
http://www.mozilla.org/products/firefox/
I know you can change the stealing focus setting for windows with Tweakui (For XP get it here
http://www.microsoft.com/windowsxp/pro/downloads/powertoys.asp}
start/ programs/ powertoys/ tweakui/ general ./focus
prevent stealing focus.
The other possibility is you are not actually minimizing them . Instead of clicking on the - are you just clicking the taskbar button? If you do this, then it sort of toggles between open instances of the program, not minimizes the window.
