Having obtained some more information, I am now speculating that the issue could be related to Roaming User Profiles, and the fact that the 360Works plugins store log files and plugin copies as dll files in the temp directory, which, depending on network connections etc, may be either local or roaming.
It would be very useful to have more detailed information about how the 360Works plugins handle Roaming User Profiles, in particular in the context of network connection changes, computer sleep, VPN log-on/off, etc.