I've tried reinitializing the apmanualcheckheader and apmanualcheckdetail and I still get the same message.

The task referenced in that message is:  

Accounts Payable > Check Printing and Electronic Payment > Invoice Payment Selection or Check and Electronic Payment Maintenance.  If you run the Invoice Payment Selection task and the Clear button is enabled in the lower left corner of the dialog then there are entries in progress.

You can use the Clear button in that task or go to the Check and Electronic Payment Maintenance task to see the entries.

The tables you reinitialized are the tables for Manual Check and Payment Entry.  The tables for Check and Electronic Payment are:  

AP_CheckHeader and AP_CheckDetail

It would be preferable to clear any entries using the Clear button in the selection task.  Reinitializing tables will leave invoices marked as paid today.