I guess I should clarify that after choosing Pay Purchase Invoices - I chose the correct supplier in the Pay to the Order of field

Morning, is it possible when you entered your invoices that it didn't say "Pay Later"? But possibly said cash or a credit card instead?

This just happened to me as well, and I struggled for a bit.  Once you have checked that it was posted in the purchases journal as "pay later" then go to payments journal, and click on  "view", then hit restore window and it should reset the columns so that you can see the invoice #, original amount, amount owing and the payment amount.  I'm not sure why it reset on me, but it is fixed now.  Hope this helps someone else.