I always have to close out firefox and start over so don't know if all the items I want cleared are gone!
How are you doing that? Do you have the automatic clearing set up or are you using the clearing from the Tools menu?
That can be caused by clearing the cookies via "Clear Recent History".
If you use "Clear Recent History" to clear the cookies then Firefox also tries to clear the cookies from plugins like Flash (LSO) and starts a plugin-container process for each plugin and that can add extra time and can cause an unresponsive script error to appear.
Make sure that all plugins are up to date.
Is cookies checked in the Clear Recent History settings?
If it is then try to exclude the cookies and remove them manually.