YES!  I had this problem and FINALLY realized that the bill payment was coded to the expense category, not the credit card account.  I had already entered all the individual charges to the expense category, so of course the payment has to be coded to the credit card account, not the expense item.  :)  Took me a lot of comparing older bills and payments to finally see the difference and why it wasn't showing up in the reconcile screen.  Hope this helps someone!!