Kristine, interesting update here...

So, I kind of made it work, but there's a bug. Maybe you can help.

The client has 7 open invoices that each range from $150 to $3000, but total approx 6500.

The client also had 62 cents of un-deposited funds from sometime before (as if they had overpaid an invoice in the past.)

Today the client made a payment to me of $1750.

Earlier, when I tried to manually apply the $1750.62 to a variety of invoices, the deposit was not working and would not go into my cash account. 

But moments ago I ignored the 62 cents and clicked Auto Apply with the $1750 payment (not what I really want, but it was a test) and it worked. The $1750 shows in my cash account, and the client's balance is reduced.

So the Auto Apply worked, but manual apply (with also using up the 62 cents) did NOT work.

Thoughts?