This issue has been bothering me for at least half a year, and others too: If you open a page in Firefox that contains Flash content, the current Firefox window will lose the focus to some other window depending on your mood, the moon phase, and the current value of Guid.NewGuid().
After updating to Firefox 18 and Flash 11.5.502.146, this behavior does not show anymore.
Did they really fix? *sigh*
It seems not. I’ll try the fix posted on Mozilla support #929688:
Open Notepad in Administrator mode, and open c:\windows\SYSTEM32\macromed\flash\mms.cfg (32bit) or c:\windows\SYSWOW64\macromed\flash\mms.cfg (64bit), and add the line