The internal degausser is not as strong as the external degausser. The external, used incorrectly, can mess up your TV tube so that it takes repeated degaussing to clear the problem.

I would remove those latch magnets and just let it be, watching to see if the situation gets better or worse. You should hear the boing EVERY time you turn on the TV, though; if not, the internal degausser is not working properly.

I still have trouble believing that an IR power command could turn on the set without the degausser. You might just have to take weeks to figure this out, not using the discrete command at all for this time, then doing it again. Be sure to come up with an answer while the set is still under warranty.

Another approach just occurred to me, which is to program a toggle power command into your remote, that is used just once when you turn on the system, then find the sony SYSTEM OFF command in the Pronto files section. Your OFF macro would use that command, so even if the toggle put your system power commands out of sync, powering down would put it back in sync.