I am experiencing the same thing and this is absolutely unacceptable for how much we pay.  We now have over 80 pages (80 pages at 50 payments per page) of payments to parse through and create these deposits manually.  Every time QBO rolls out an update something like this happens.  

To be clear, this is an issue with the recording of the deposits in QBO.  Nobody is having an actual problem with the funds being deposited.