OK here's an update. I formatted and reinstalled Vista, and guess what? I am having the same problem.
If I run with no add-ons everything is fine. But there are no add-ons enabled when I run it normally, so I don't see why there is a difference.
If I run as Administrator (I still don't understand this feature - I AM the administrator...) everything is fine - with add-ons enabled.
I installed the Google Toolbar, which I had removed to try and fix the problem, and even with it installed, IE works perfectly when ran as Administator, but not when ran normally.
My "start page" is a custom HTML file, and the first time I clicked a link from it, I got this message:
"Internet Explorer needs to open a new window to display this webpage. For your computer's security, websites that are in different security zones must open in different windows."
I have all popups set to open in A NEW TAB IN THE CURRENT WINDOW, but they just don't do that! They open in a new window instead....even with a normal left click, which should just change the page. And if I click my "Home" button from any web page - it opens in a new window for no reason.
I think this "security zones" issue must be the cause.
Edited by tomdrayson, 24 February 2007 - 11:10 AM.