This may occur when you run your Post Revenue to GL process either before or at the same time as you run your Deposit Process. 

To ensure all transactions are included in your Deposits:
1. Run the Deposit Process daily or prior to when you run your Post Process.
2. Make sure the Deposit Process is complete before starting your process to Post Revenue to the GL. 

If you find that transactions are still not pulling into your deposit, please Chat with Support and reference this article.