I look at my web host control panel and it says I'm using 1.1 gigs of disk space. This sounds completely ridiculous, there's no way I'm using that much space. So I used my FTP program (SmartFTP) and went through all my directories checking the file sizes and totaling it all up. It's just an estimate, but it looks like I'm using around 300-400 mb, no where near the amount my web host control panel says.

Anyhow, I want to make SURE I know how much space I'm using before I approach my web host about over disk usage accusations. Is there any program out there that can tell me for sure how much space I'm using? I'm sure this web hosting company's control panel is wrong.

As an administrator, I would check your usage from the command line.

Otherwise, Im not sure what else to recommend. Contact them, and ASK them to check your usage on the system outside the CP. Let them know you feel the CP might have an error, and that you total the usage differently. If you contacted me with an attitude, or 'accusations' I would tell you to piss off, if you asked nicely I would run and check it for you asap.

If your with a company you can't trust to give you a honest answer, then you shouldn't be hosting with them at all.

All your webhost needs to do is run the fixquotas script.. that should solve it.
However check the disk usage in cpanel to make sure that you haven't made a mistake.