Have a case opened but wondering if anyone else has seen this:
After the upgrade from ru1 to ru3(including the point fix that was released) if you start a pxe rebuild all of the sites will get the green arrow on them like the rebuild has been deployed. On the NS bootwiz.exe will kick off and the new files will get created, but at no point does the recreation process start on the NBS sites. To get it to run and show completed in the console you need to remove the NBS site service from each location, wait for it see its been removed then add the service back to those sites, after awhile it will kick off the recreation process and the console will show the site as completed.