In a previous entry, I described how (and why) to delete the preference file automatically as InDesign, InCopy, Photoshop or Bridge start up.
Well, it turns out that this works in Illustrator also. You just don't receive a confirmation dialog box in Illustrator that anything has happened, but your Illustrator preference file will indeed be deleted. Just hold down the same key sequence (command-option-shift-control (Macintosh) or control-alt-shift (Windows)) immediately after you click the Illustrator icon to launch Illustrator, and keep holding the keys until Illustrator has finished starting up.
If your copy of Illustrator is misbehaving in any way, this is always the first thing to try. The only downside is that you will lose any custom settings that you have applied in the Preferences dialog box.