Payroll Reports Incorrect with the new billing format

I'm running payroll for my team members and the income allocation reports are incorrect. I see several things that are creating issues:

*If there is an issue with a claim from insurance, an invoice will be populated for the cash rate and then that ends up as a negative amount in that client's invoice and therefore is subtracted from the clinician's payroll, even if the insurance claim is corrected and paid. Therefore I have clinicians who are having $180, and $150 subtracted from their payroll incorrectly.

*This new system is creating many unallocated amounts. These unallocated amounts are not being included in payroll and there is no way to catch this at a practice-level upfront. You have to go to each individual's chart to find that there is an unallocated invoice sitting there.

*Another issue -- refunds -- I issued a ton of refunds to a client whose insurance claims came back and issued these refunds against their initial session. Therefore, it should have automatically allocated this amount to the session in which I was refunding it. Instead, all these amounts ended up "unallocated". I then had to go back and reallocate these amounts to the sessions, I had already designated. 

I am pretty computer savvy and had a lot of mastery over the previous version of billing/payments and I am finding myself spending hours now doing payroll and cleaning up billing problems.