It's really imperative to have good, steady current via battery charger. Not absolutely necessary, but it helps.
Edit: I'll add that maybe that's not your problem, but in my experience (limited), that has cured 95% of any issues I've had.
I did notice this. It was at the point that I connected the charger that I began having issues, or so I thought. I read somewhere that "smart" battery chagers induce interference that ecu's dont like sometimes. I may have had the wrong memory layout selected as well.
On the final run where the ecu did finally flash I started having block flash errors and having to retry, the moment I hooked the battery charger up it flashed like butter. So evidently I found the 'magic' combo of correct layout, correct laptop and enough voltage to make it happy.
I am relieved to say the least.