Mail disk usage Limit

I’m having a problem. A couple of the e-mail users on my sites have reached their inbox limits. So I went onto Squirrel mail and cleared out their trash, their sent e-mails and the like. Anything to get their quota down. the server is still reporting, though that their inbox is 90% full. Am I missing something?

Everything I’ve checked has been through Squirrel Mail. Can they save to the server through Outlook or something similar? Where else on the server might I check?