Thanks for the reply. I've tried all that were suggested in there. Not sure what you mean by your last question, as in plug-ins? Theme perhaps?
As a theme I have ChaosTheory. As plugins: Bad Behaviour, Contact Form Manager, Donation Thermometer, Hide Category, One-Click Child Theme, SEO Ultimate, Ultimate Category Excluder, Who's Amung Us and WP Database Cleaner.
The category manipulation plug-ins aren't the ones causing the problems since I tried disabling them and it doesn't fix anything...