In some instances, the Deposit Processed flag was not being set due to total amount of payments and credit memos applied being cents (ie 0.002) off from the expected total amount due. This issue has been fixed. Whole dollar amounts are now compared.
The Deposit Process flag is set to true when the sum of approved/entered/downloaded credit memos and approved/approved credit card/entered/downloaded payments equals or exceeds the amount defined in the first payment schedule item.