I've seen this behavior when I've set up AUTOPAY at the credit card company.
I'll get a statement, reconcile the Quicken Account, then enter the payment in the amount of the statement balance in the checking Account. When the check clears it's frequently for a lesser amount than the statement balance, and that happens becuse the credit card company subtracts returns (refunds) from the statement amount when they pull the funds from the bank.
Could something like that be going on here?
Is the check always less than the statement amount, more than the statement amount, or randomly higher and lower? If the payment is lower than the statement amount then it seem like you'd be incurring some interest expense on the credit card, unless it's lower because of "returns."
I've not used Quicken's payment service since it does seem to be a common problem topic in here. If you really want to figure this out then I"d say you'll have to contact Official Quicken Support and have them look into it. I've set my wife's Discover card on autopay with Discover and that's been rock-solid, haven't had a problem.