New Credit Card account impacted Checking reconciliation

While adding the credit card account, did you download transactions from the bank into this account?
If so, did the downloaded transactions contain payment transactions for the credit card, as transfers from your checking account (categorized as "[name of checking account]")?

These payment transactions, when accepted as transfers, will have created duplicate transactions in the checking account, thus throwing off your checking account's balance.

Look for these duplicate transactions and delete them from the checking account. This will also delete them from the credit card account.
Now, in the checking account, look for the original credit card payment transactions. Change them to become real transfers, categorized as "[name of credit card account]". This will make the payment transaction reappear in the credit card register.

If you have correctly made these changes, your checking account should balance/reconcile again. So should your credit card account.

Don't forget to change the scheduled reminder or Memorized Payee List entry for your monthly future credit card payment transactions to become a transfer transaction, categorized as "[name of credit card account]"