This isn't a huge issue for most of our customers, but while updating my personal BR2, I couldn't get a connection to either a Purple or Black Cube while I could with a 3DR Pixhawk1.
All autopilots were updated to 4.0.1.
Tested with 0.0.19 on a 3B and 0.1.0 on a 4B.
This may be related to the autoconnect issue with these types of boards (got fixed in QGC v4.0, but the drivers may not be in Companion): mavlink/qgroundcontrol#7261