In the Bank Account History page the 2nd column is headed "Ref No." above "Type". What is the source of the "Ref No."?

It is the transaction number, jpjmflanagan. 

If you're seeing a number above the transaction type, let's say it's an invoice, the "Ref No." is the Invoice no. If there are no numbers above the transaction type, that would mean the transaction has no cheque, sales receipt, or invoice number.

When you click on Edit to view the transaction, you'll see the same number under the reference column and on the transaction window. 

Just let me know if you need more help. Have a great day!