MS commonly roll out Xbox 360 updates in small doses. rather than blast out a full firmware update all in one go. So I wouldn't be surprised if this actually is related to the new disc format, but being caused by one of the small incremental updates that MS like to release.
It seems strange that MS would need to send someone a replacement console rather than just roll out another update. Either the update has somehow irreversibly borked those few consoles or this is Microsoft's subtle way of replacing all the consoles that cannot have their drive firmware re-flashed with the new security protocols (or perhaps a specific model of DVD drive has a vulnerability that could be used to break the new security measure).
While it's a bit Big Brother, I do like how MS were able to detect people having problems over Live and pre-emptively get a new console to them. Perhaps they should look to detect RRODs, etc as well to make the repair process a bit quicker/easier?