Update: As Skassa said, when you power the main relay the first time you get bootloader. Then only if you quickly turn it off, then on again, will the ECU boot up normally. Odds were simply electrically better with a powered USB adapter connected.
All electronics are powered through a B+ post on the firewall. We tried removing the MSD CDI ignition box (MSD 6A) from this post, no difference.
I've never seen it before like this. It was never an issue with the old ECU with everything else exactly the same (harness, and all).
Any clues on how to solve this issue?