USB ground loops like this explain all the issues, but this also adds to the fact that the ground connections were way too thin in many areas. That said, eliminating the ground loop issues is not really the job of the shield, as they're an issue with your PSU/PC/Due config.
Just submitted to bobc a major overhaul that provides a lot of thicker ground traces (with multiple redundant paths), plus extra thickness to almost all the Ground, +V_LOGIC and +5V traces (there are a few exceptions that I'm hoping to eliminate at some stage soon).
Just submitted to bobc a major overhaul that provides a lot of thicker ground traces (with multiple redundant paths), plus extra thickness to almost all the Ground, +V_LOGIC and +5V traces (there are a few exceptions that I'm hoping to eliminate at some stage soon).