There are a number of system cache and temporary files that do not get completely purged until you turn off the Mac. During a restart, power is still supplied to all the hardware components (RAM, HDD, Graphics cards... etc), so problem files can still hang around, or harware compoments (which can also cause problems) are still powered up and not reset by a restart.
For example - A customer called complaing that the fans in his mac were running full speed and would not stop. I told him to shut down the mac, but he only restarted it, and the fans stayed at full speed. I told him he needed to actually shut down/power off the mac, wait a couple seconds, then start up the mac. That fixed the fan problem, and he was happy.
There are also those rare occations when even shutting down the mac does not reset components, as even with the mac shut down, there is still power to the system. In that case, the Mac has to be physically unplugged from the power outlet, and left to sit unplugged for several seconds.
Another. let techy way to delete/reset your prreferences is to use a great free utility from Digital Rebelliion:
Preference Manager
Preference Manager allows you to manage preference files for Final Cut Studio, Final Cut Express, Final Cut Pro X, Avid Media Composer and Adobe Premiere Pro for Mac.
Preference files store information about user preferences, window layouts, toolbar placements and launch settings. Sometimes these can become corrupted, causing problems. Preference Manager allows you to trash corrupted preferences and keep backups of working preference files in order to quickly restore your settings.
PM will allow to specify only the STP files or the entire Final Cut Studio or just delete a single file at the application level.
Glad you got things working.. 🙂