I hope this isn't an indication that Ducati has added some kind of ECU overwrite protection on the 1299 ECU. There are workarounds to such protections, but how is far beyond my understanding.
When the ECU to my Audi RS6 was reflashed, the tuner had to do it in small chunks, because Audi has some sort of ECU protector that shuts it down if it's being overwritten for longer than a set period of time (maybe 30 seconds or something like that).
Audi now owns Ducati; it's possible they started write-protecting the ECUs. Tuneboy needs to determine this for certain before releasing 1299 files; imagine the uproar if everyone who tries to overwrite 1299 ECUs ends up bricking it....
I beleive Tuneboy tested their initial 1299 stuff over a month ago on a bike in Germany so hopefully that's not the case and I'm sure they would be aware of any issues.
The guy I'm using for tuning who has some dialogue with Tuneboy is still waiting for the 1299 files (as we all are!), hence I wondered if they'd flashed an old file by mistake. Anyway, glad it's sorted, hopefully an isolated incident.