What Toolbars and other add-ins do you have installed? Do you open one tab or more than one (look in internet options for the default window)? Is your IE set to restore the last window on open or open default?
Yes, this can happen with rootkits, etc, but these other areas can also cause the issue.
Just for grins, while you are checking configurations, do you have anything you don't recognize in your startup (I like CCleaner/Tools/Startup rather than MSConfig because I can disable and re-enable line items easily)? Using the CCleaner ( www.ccleaner.com ) to address the startup and letting it do a good clean of your tempfiles, etc. might be a good additional step (on the theory that a tempfile may be re-launching when you open the browser).