It sounds like something is setting your browser to run when Windows starts. I would begin by checking your startup items using MSconfig and look for anything that could be opening IE or that you don't want running at startup and uncheck it.
You can also change some IE settings to try and prevent this from happening in the future. From IE click on Tools, Internet Options and then the Advanced tab. Under the Browsing section make sure the boxes that say Automatically recover from page layout errors with Compatibility View and Enable Automatic Crash Recovery are unchecked. This is more of a workaround and you may want to try and uninstall/reinstall Internet Explorer to see if it fixes your problem.