First, you might have a look at the mailbox sixes in Exchange Administrator. This is a good reality check to make sure you don't have a rogue mailbox out there with no size limits. If nothing stands out, it could be database corruption. You might take the database offline and then run database utilities on it to see if it is corrupt. Additionally, you might want to perform an offline compaction to see if that shrinks the database file for you, too.
Before I run any utility or process against my Exchange databases, I like to take a copy of them and put it somewhere safe. This way if my utility or process does something bad to the database, I have a backup copy to fall back on.
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