Hey,
Im sure someone knows the fix to this because its a very common problem but I cant remember what it is you do.

Which script do you run to recheck the space allocations in WHM?
Ie. WHM is showing Space Used as 0mb for all accounts so I have to fix that to see whats actually being used

/scripts/fixquotas

Got it,
Just incase anyone wants to know for the future

That would be it.

When you are in WHM just click "View disk Quota" or somthing like that under the client managemt part where it shows you everyones quota, and it says what script to run to fix it

incase you ever forget just look there.

Thanks Nick, I didnt even know about the link in WHM before!
First time I had the problem in WHM, only done it because the log was really big from cPanel and I needed to fix it to check how much space was actually being used by the accounts

Yea, theres alot of stuff in whm. I suggest you just take like 30 mintues when you get a chance and just go through every page of WHM and see whats there and what you can do.