I ran a repair as suggested, thanks.
I've looked though the error_log to see what, if anything, has been going on. The mysql error I've been seeing is:
[15-Oct-2007 12:28:47] PHP Warning: mysql_connect() [<a href='function.mysql-connect'>function.mysql-connect</a>]: Too many connections in /home2/*account_name*/public_html/filepath/dbconnect.php on line 6
When I saw this happening I logged into the server right away and noticed it said "MySQL Databases NA / unlimited" under the General account information, also the phpMyAdmin displayed an error in big red font when I tried going onto it. After a few minutes it fixed it's self and I thought nothing else of it. Then I saw it happen again but once more it fixed it's self. My users told me it had been happening for days and the lag was unbearable and the downtime was annoying bla bla bla bitch moan cry etc.
Since then I haven't seen the error or experienced any problems.
The only instances of this were all encountered on the 15th. It hasn't been going on for 3 days at all. I will have to have a talk with my users and thank them for making me look a fool.
Apologies.