When making a new window firefox behaves differently than the first instance.
Im not sure why but after upgrading to FF 6, when you open firefox the tabs are above the address bar which is normal. but if you create a new window the tabs get moved below the address bar and the address bar doesnt work properly.
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Try the Firefox SafeMode to see how it works there.
A troubleshooting mode, which disables most Add-ons.
(If you're not using it, switch to the Default Theme.)
- You can open the Firefox 4/5/6/7 SafeMode by holding the Shft key when you use the Firefox desktop or Start menu shortcut.
- Or use the Help menu item, click on Restart with Add-ons Disabled... while Firefox is running.
Don't select anything right now, just use "Continue in SafeMode."
To exit the Firefox Safe Mode, just close Firefox and wait a few seconds before using the Firefox shortcut (without the Shft key) to open it again.
If it is good in the Firefox SafeMode, your problem is probably caused by an extension, and you need to figure out which one.
http://support.mozilla.com/en-US/kb/troubleshooting+extensions+and+themes