Bill payment amounts involuntarily reduced

So I have been having a frequent problem where a Quick Pay credit card payment I have set up long in advance has the amount "rejected" on the day of payment and a payment for a lesser amount is made.  I get an email from Quicken saying something like "Payment completed, Amount Reduced".  

This was very confusing at first, but after several occurrences, I realized that this is occurring when there are any other credits on my bill during the month.  For example:

Balance due on monthly statement: $1000
I set up Quick Pay payment for $1000.
A couple weeks later, I get a merchant credit for $5.
A week later, my payment date arrives, and my $1000 payment is rejected but a $995 payment gets made.

This is super annoying, because none of this gets automatically fixed in the register, so I end up with my original $1000 payment in the register, plus a new $995 payment that gets downloaded from the bank, and I have to manually fix it all.

Eventually I *think* I figured out that this only happens when I've chosen (in the Quick Pay window) to pay the "entire balance", and so I started selecting "Other amount" and then entering the entire balance amount there.  That seems to solve the problem.  BUT:

Some accounts don't come up with the three options in Quick Pay (Entire Balance, Minimum Payment, Other Amount) and only have a single amount field.  On those accounts, this problem keeps occurring and there seems no way to fix it.  

There is really no justification for changing the amount of a payment that has been set up, and I hope that Quicken can find a way to eliminate this behavior.  

It's super annoying.  The only MORE annoying issue is when a long-before-scheduled Quick Pay payment suddenly and inexplicably fails on the day it's supposed to be paid.  That problem will be the subject of another post.