Thanks for your suggestions; however, 

All of the dates match, or are within a day of each other. 
The amounts on the deposit match what I have on the sales receipt. 
If I’m looking at the right spot, I’m not seeing anything that’s been reconciled. 
Multicurrency is not an issue. 

Is there something else I need to look into? When I set up the daily receipts, I feel like I set something up wrong, once I fixed it, it appears  to have corrected itself going forward, but not on anything that had already been done.