I think I’ve done all my homework - 64 pages of search results throw up around half a dozen identical issues to mine with no consistent solution:
Mission Planner 1.3.10 on Windows 7, USB connection with 1A of current available. Arducopter (no peripherals connected other than USB) Repeatedly fails to complete reading phase - halts at about 80% saying “Communication Error - no connection”. MAVlink will however connect just fine so USB drivers/virtual comm port all operating as expected. I checked the properties for the comm port to make sure it was set to the same baudrate 115200. Comm port number is quite high (22) but it doesn’t hinder the MAVlink connection. The only other thing I can report is that, to begin with, detecting Board Version takes around 20 seconds which seems a bit long and may hint at something.
Oh, and I almost forgot - APM Planner 2.0 rattles through the same procedure without a hitch. I think that points to the software rather than the hardware!