I'm having the same issue. 

I reconcile my parent account every month with no issue.  However, I don't do anything with the subaccounts and they do have balances that need addressing.  I've read the previous replies, but I'm still confused about the "next steps" I should take to fix this issue.  One post said to reconcile the subaccounts, another said to move all the transactions from the sub to the parent, another said to create a journal entry to move the balance.  In the subaccounts, it looks like the transactions have been reconciled as they have a check or a lightning bolt next to them (we use bank feeds.)  The transactions seem to be showing in both the parent and the subaccount, so I'm not sure what to move.  What would the journal entry look like if I created it?  Moving the balance from the sub to the parent account would make the total owed WAY off from what is actual.