The first thing to check is to be sure A/P is integrated with Bank Rec. Go to Accounts Payable, Setup, A/P Options, Main Tab. If Bank Reconciliation is not checked, select the box. Your post mentioned a manual check but did not mention if regular A/P checks are posting to Bank Rec as well. If integration was not turned on, you can enter the check in Check, Deposit and Adjustment entry. Since the check should already be in the General Ledger, you don't want to post the entry to G/L. If you find that the G/L integration is also turned off, I recommend you contact Support for further assistance.

When you are in clearing checks, do you see the check there?

If it is there, does it have the correct date?