I tried using the new multi-bill-to deposit function today.  I had 2 invoices from 2 different bill-to's on the same check.  Keyed in full check amount, applied 1st invoice.  At end, went through screens and answered "Yes" when asked if I wanted to apply balance to a different customer (bill-to).
 
When deposit screen appeared, showed "Continuing check # xxxx" at top.  Good.  Balance of check at bottom, though, showed entire check.  Applied money to 2nd invoice.  Still showed balance of 1st invoice as unapplied balance.  When got to end of deposit, answered "No" to apply balance as customer deposit.  Application ended.
 
GL for cash now out of balance.  System removed invoices from open AR list, relieved AR, sales commissions, and customer earned discount in GL, but no cash was posted to the operating/bank account.  Had to post journal entries to operating GL account to get back into balance.
 
No idea what happened or why it did this.  Any ideas?

Fantastic!
 
I wasn't sure if I was doing something wrong or not since I had never used before.