Under Cash Transactions and Bank Transactions tabs, the reference column is sorted as text rather than numbers.
For example, instead of 1 - 2 - 4 - 10 for an ascending sort, you get:
By contrast, in the Sales Invoices tab, the same sequence sorts as numbers:
I have not checked other places where this problem might exist.
EDIT: After further thought, it occurs to me this might be by design, to allow sorting of references if alpha characters are included. This could be important for bank transactions, since the user has no control over a bank’s reference content.