Is this AR or AP?  I would extract the transaction payment history files and see if there is a record in there.  How old are the invoices.

It's AP. I found out that the total invoice amount was entered into "subject to discount." I'm guessing that's why it shows up under invoices but not in transactions and not on my P&L. For now I'll just journal around it. It's just odd that it still showed up to be paid. And I've found at least two invoices that this happened with. Not sure how to find out if there are more! Sage gives me a headache.

It's AP. I found out that the total invoice amount was entered into "subject to discount." I'm guessing that's why it shows up under invoices but not in transactions and not on my P&L. For now I'll just journal around it. It's just odd that it still showed up to be paid. And I've found at least two invoices that this happened with. Not sure how to find out if there are more! Sage gives me a headache.

Well - it turns out that's not it either. Oh well. Back to the search.

Go into the GL, Main, Daily Transaction Register.  You may have unposted GL transactions. 

Thanks - but I did check that. I found it's just one AP posting so that is a relief.

I would extract the AP_OpenInvoice file and see if the invoice is there and what the various fields say