I contacted support about this and they suggested I post this here as well....
I dragged and dropped several transactions from a Visa register to a Mastercard register as they had been put in the wrong account. However, I accidentally dragged one that was already reconciled instead of the one I wanted without realizing at the time. This caused the Mastercard to show a difference in the balance, when I tried to reconcile it. It was not easy to find. Finally did by searching for the amount in the register as it did not show in the reconcile window, due to it already being reconciled (although in a different register). Once I found it, I finally remembered what might have happened and sure enough, moving it back fixed it.
For a fix, I would suggest having a warning dialog pop up when someone tries to move an already reconciled transaction from a register. Similar to what happens when you try to modify already reconciled transactions.
On a second note, when reconciling an account, it would be nice if the split would NOT automatically expand when I check the box.
That is all...