My understanding is there is some incompatibility with the ATO system, possibly regarding accurate stopping at stations, although there's just no information given out at all about the issues and financial loss resulting, not even to the London Assembly, who seem to show no interest or ability whatever in determining what the problems are.
Potentially fixable by changes to the system rather than the trains, but that of course also drives the existing trains, so those have to be tested as well on the changed commands. There were some notable speed reductions introduced some months ago, particularly on downhills, which were glossed over with a statement that the "existing trains had been overspeeding" in ATO. Unnoticed for the last quarter-century, apparently ...
One wonders what credence was given to placing the new train order with Bombardier, who did the existing stock and know all aspects, rather than with someone, possibly a fraction cheaper, who had never worked with it before. And has any cost saving now all been lost.