This is actually similar to bug 296614, which referred to the ledger scrolling to the bottom after merging two transactions.  That was fixed by leaving the focus on the next transaction if the action deleted the transaction under focus.  However there are other cases where the ledger scrolls to the newest transaction after some action, instead of remaining focused on the previously selected transaction.  This always happens at the end of reconciliation, even though I would prefer that focus remain on the last transaction prior to or on the reconciliation date.