If 2 windows are open, opening a new tab in window #1 opens in window #2 and vice versa.
If I have 2 windows open (different sites in each window), and open a new tab in window #1, the new tab opens in window #2. Similarly, if I open a new tab in window #2, it opens in window #1. Never had this problem in any prev. FF version. I am running Windows XP.
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Do you have that problem when running in the Firefox SafeMode?
A troubleshooting mode.
You can open the Firefox 4.0 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.
To exit the Firefox Safe Mode, just close Firefox and wait a few seconds before using the Firefox shortcut to open it again.
If not, see this:
http://support.mozilla.com/en-US/kb/troubleshooting+extensions+and+themes
Are you using multiple (two) monitors to display those windows?
It seems that changing the "Persona" has solved the problem.