IT bogging down my computer all of a sudden

I've used IT for almost 2 years and never had a problem until 2 days ago. We ran a CHKDSK on the computer and since that time, everytime I hit a key in any program, IT is doing something (not sure what) and it slows the process down - sometimes making me wait up to 2 minutes just to do a simple keystroke. I've checked every menu item and nothing appears to be different. I even uninstalled and reinstalled it and it still is bogging my system down. I know it's IT causing the problem because when I don't load it, all programs work very fast and are not bogged down. It's very difficult to work since I use a platform that requires clicking on various icons for pt lists, etc. but it's impossible for me to work without IT because I've become so attached to it :) Is there anything that would cause it to be running something in the background that I can't see? Any help you can give me would be greatly appreciated.