When using Firefox 3 Beta 3, a Extensions folder is left behind in the Application Data folder.
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do you use? I use beta 4 and don't find any extensions to recreate your problem.
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This was an issue with 3 Beta 3. The launcher for 3 Beta 4 has been updated to handle this directory.
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I upgraded to Firefox 3 Beta 4 and the Extension folder is still created on every run. Another folder called Crash Reports is also created on every run.
It's created and then removed on exit. Unless firefox.exe gets hung and can't exit (Task Manager and kill it then FirefoxPortable.exe can exit and clean up). Which seems to happen relatively often in Beta 4. But that's why it's a beta.
Sometimes, the impossible can become possible, if you're awesome!