@greyhairweenie - sounds like you might have another client accessing your mailbox at the same time doing the filtering. If it is SquirrelMail doing that, you'll need to find the filtering rule that tells it to move some messages to the Junk folder. SquirrelMail doesn't do that by itself - you have to tell it to. You might want to contact your system administrator for more help - this isn't a help forum.
@sirmafia -- SquirrelMail has a plugin that can interface with most quota systems. However, keep in mind that it's your responsibility to build a quota system into your mail server first -- SquirrelMail is only a mail *client* and does *not* manage user mailboxe. It will interface with your system and report the quota information in the webmail interface if configured correctly. See: http://squirrelmail.org/plugin_view.php?id=237