What you may be experiencing:
Selling item from their Customer Order, then adding Shipping to the Sales Receipt, causes the Customer Order to show a negative balance.
What you can try now:
You can add Shipping Charge to the Customer Order, prior to taking Deposit and selling the items off the Customer Order.
At this time we have to re-prioritize this issue to gauge the customer impact. We do our best to resolve as many issues as we can identify but have to focus on those that have the largest impact. At this moment we do not have any updates, as we have new and relevant information we will communicate that out.