As an experiment, you might try setting _BESClient_Resource_StartupSleepSeconds to 300 seconds.
setting "_BESClient_Resource_StartupSleepSeconds"="300" on "{now}" for client
There’s a description in the thread below. What I would speculate could be happening is that during the Windows Setup phase, while the system is still in the “temporary” Windows installation and finalizing Setup, the BES Client service could start up and send a report. Then when Setup replaces the permanent registry with the upgraded registry, that could roll back a client report sequence number and force the client to reset itself. It’s been a few years since I’ve seen that as a problem, but it might be worth a try.
edit: smart quotes