That’s been my experience as well. I’m not sure whether there is any good option.
This isn’t authoritative, but it looks to me like during Windows Setup, when we’rw in a temoprary Windows environment, the BESClient starts up and sends in reports. The Setup process then restores the original registry HKLM\Software hive into the “new” Windows installation - including an old BESClient report sequence number (which is lower than the sequence numbers the active service is now sending).
Then, when it reboots into the “New” windows installation, the BESClient reads that restored registry key and sends duplicate report numbers incrementing from that old, restored sequence. Since the reports have duplicated numbers the server tells the client to reset itself.
It might be possible to prevent the client from sending reports during the Windows Setup process, but if something went wrong and Windows Setup hung or was left prompting from some user input, and the BESClient isn’t running, the system might be left unmanageable. Or you might have trouble re-enabling BESClient after Setup completes.
I’m not sure how I’d try to work around that, so I ended up accepting it in my environment and tried to skip every other Feature Update so we did them less frequently.