I am having this issue as well.  Mine is random though.  I will print a check, click that it printed properly, and go on to the next bill.  When I go to print that check, the check that I had just printed is there waiting to be printed (even though it was already done) as if I hadn't just done it, and "print later" is checked when I go to the account and look at the payment.  I hope that made sense...