I, too, have this issue and have not yet found anything telling me how to get rid of the problem.  Has anybody dealt with this before?

I have figured it out.  Took some digging, some trial and error, but I have figured it out.
 
Use Maintain Database (System Manager, TAS-D) to find the invoice(s) listed in the BKAPINVT file and make note of the Invoice Number (BKAP.INVT.NUM), which is actually a reference number for the transaction.  Also, make note of the other parameters (I found my error in BKAP.CHK.INVDTE) for the transaction as you will need them for the next step.
 
Then use Maintain Database to open BKAPCHKH and find the payment(s) associated with the invoice (based on the vendor code and invoice date).  Make sure that the Invoice Number (i.e., transaction reference number) is identical to the transaction number listed in BKAPINVT.  Also check your other parameters, such as the BKAP.CHK.INVDTE parameter (that is the check date/payment date parameter).  If they do not match, edit the parameters so that they match those in the BKAPINVT file so that the AP Aging program can match up the two transactions.
 
I sure hope this helps others who have been fighting and struggling with this problem for YEARS!