Recently our WSUS server crashed and we had to rebuild it. We have several replica downstream servers in branch offices all configured already to auto-populate the groups for each office. I had to recreate these groups and several of the downstream servers. Anyway, many of the downstream servers have synchronized correctly and the computers in the groups those downstream server control have put the computers back in their proper groups. About 15% of the computers are still sitting in the unassigned group under their respective downstream servers.
On some of the downstream servers I have changed them to allow me to move them into their groups and then changed it back to allow group policy to do it. I then manually synchronized several times to no avail. The rebuilt WSUS server has been in place for several days now yet nothing seems to be moving anymore.