Can you update the weight of the digital good to 0? A shippment with 0 weight should have a 0 charge.
It may be that we only tested for either digital or physical goods and not a combination like you are using. We may have to fix some issues to get it working, but we will work with you to make sure we get this working as you want it. We'll probably have to work with you directly in a connect meeting. I'll create a support ticket so that we can share information privately and schedule a phone call.