We have been using 2.0 for several months now and it's been working great. But just now we had an order go through with no shipping cost charged. It looks like the correct method was selected (Standard Shipping, which is the only choice for orders within the U.S.) but the shipping cost was $0, when it should have been $47.95. In trying to replicate the order (using the same items and the customer's address and everything) I cannot get a zero dollar shipping cost to happen. I can't even deselect the shipping method. It looks like it's all working as normal. I also checked the error log and there are no errors from today.
We talked to the customer, who said that there was a shipping cost showing "on the screen before," which could mean in the cart before going to checkout, or on the checkout page before submitting the order. Sorry she couldn't be more specific than that...
We do have some fairly complicated custom shipping logic, which I could share if that would be helpful. (It's quite long.)
Any ideas would be great!