"Every couple of weeks I have a mystery deposit show up in my checking account from my employer for about $900."
I'm assuming that you're referring here to your Quicken checking Account, i.e., it's not a real entry that you can find in your actual checking account with the bank. If that's the case then the logical place to look for its origin is Tools > Manage Bill & Income Reminders. Did that "one time" expense reimbursement somehow get set up as a recurring entry?