I was familiar with this issue from earlier, when it had affected nearly 100% of our Windows 2000 server population. Then it was due to an .MSI (patch msi) install not being finished due to a silly error message (it missed something from the package).
Clearing the plugin flag did not work, since the problem then recreated afterward when the patch msi was run again.
And I never thought that it would appear on Windows 2003 servers and "latest" MA version, too. :-(
Thank you Joe.