The Credit Note issue is one I have brought to Softrak's attention a number of times, as recently as this week. Their reply is "This issue is still in R&D."

In the meantime, as a workaround, if you catch the JC billing batch before it posts, you can go in and modify the credit entries to change the type to Billing instead of Other Charges. If the entries have been posted, you can enter a pair of offsetting entries into a new billing batch, one as Billing type for a negative amount, and the other as an Other Charge type for a positive amount.