You may find that you have a payment that is marked as Do not post, and is not pulled in to a deposit. You also have your GL turned on, and the deposit is able to be posted.
Transactions/orders created during the duration when the GL is disabled are marked as Do not post, and the status will not change. Transactions that are created when the General Ledger is enabled are marked as Not Posted, and the status of these transactions/orders will be changed to posted when the Post to GL Process is run.
Steps to Duplicate
1. Go to sales > order search > search the order number 2. See that the post status is do not post 3. Go to analysis > information library > add an ad-hoc query > choose the source view of revenue 4. On the left select revenue > in the middle select check number and move to Include records where set equal to the check number 5. In the middle select deposit number move to Results fields to display 6. Preview results and note the deposit number 7. Go back to the query > delete the check number from Include records where 8. In the middle select payment method > move to Include records where and set equal to pre-altru method 9. In the middle select amount > move to Include records where and set equal to XX amount 10. Preview results and see this payment is not in a deposit 11. Go to treasury > deposit search > search the deposit number 12. See that the deposit is not marked do not post