There are command line options to use with cmdagent.exe(which is what you are looking at when you open the agent monitor) that can retrieve new polices and enforce them. you could then donwload something like P***EC from microsoft to run remote programs on a command line. Unless you already have something in place to run remote programs, which I guess with that amount of nodes you should do(TNG, Landesk etc.)
EDIT. The forum didnt like the name of the tool, it is P S E X E C
I did have this issue on a few computers at one time, I ran an agent summary report and had it also verify the managed state and the ones I had issue with were listed as Unmanaged. You might want to check the managed state of those particular computers.
There may be an easier way, but I simply reinstalled the agent on the computer using the Framepkg.exe /install=agent /forceinstall command. You can try pushing the agent to the computer using the Deploy Agent option in EPO and see if that does the trick.