My first guess is you have a duplicate Snort instance running. That can happen in some rare circumstance with rapid package restart commands.
To test this, stop Snort using the icon on the SNORT INTERFACES tab.
Next, open a CLI console session and issue this command:
ps -ax | grep snort
It should show no running Snort processes. If it does, then you have found the problem. You would need to kill the duplicate process. If you do not see two processes, report back.
The correct way to disable entire rule categories is to uncheck them on the CATEGORIES tab, then click SAVE.
Bill