Not sure if it will fix your particular issue but worth sharing anyway.
I had issues with twitter boot strap in IE. No rounded corners. Navigation menu not collapsing. Spans not sitting in correct location, even some images not displaying.
Strangely, site works okay in IE when run through visual studio debugger, its once deployed to a server that the problem occurs.
Try using IE developer tools (F12 is keyboard shortcut) Check your browser mode and document mode. (its at the top along side the menu bar)
Problem happened for me as document was IE7 and browser was IE10 compatibility. I added a http header in IIS: Name X-UA-Compatible Value IE=EmulateIE9
Now the page loads as document - IE9 standards, browser IE10 compatibility and all the previous issues are resolved.
Hope this helps.
-tessi