I'm not from IK Support, but, if I understand you correctly, I've had the same experience with one account.
My Citi Account will provide (I believe) a negative ledger balance when the balance is actually positive. I recently overpaid the account by $18.14 and the reconciliation report showed the "Difference" as $36.28. I actually have to wait for the CC balance to become negative again, before I can reconcile correctly.
I had originally thought that it was a Moneydance Problem, however, it appears to be on the Credit Card side, as other accounts do not respond the same way. Here is a previous discussion related to the matter: