Examine one of the client computers mentioned in the event for all non-Windows-provided services, scheduled tasks that run at startup, SCCM/SMS at boot jobs, computer startup scripts, or anything else that runs when the computer is restarted. Then get promiscuous network captures of that computer starting (any time, not en masse) while also running Process Monitor in boot mode, and you’ll probably see some very likely candidates. You can also use SPA or AD Data Collector sets (http://blogs.technet.com/b/askds/archive/2010/06/08/son-of-spa-ad-data-collector-sets-in-win2008-and-beyond.aspx) in combination with network captures to see exactly what protocol is being used to overwhelm the DC, if you want to troubleshoot the issue as it happens. Probably at 3AM, that sounds sucky.
Ultimately, the application causing the issue must be stopped, reconfigured, or removed – the only alternative is to add more DCs as a capacity Band-Aid or stagger your mass reboots.