I started having the exact same set of issues tonight. I have been on 5.8.4 for a few weeks.
Signed on to the admin console. A pop-up window appeared saying there are package updates available, please click Update Packages, etc., which I did. After a couple minutes another pop-up appeared saying the update was complete and I should reboot.
When the reboot was complete, I signed back on to the admin console (the eisy STILL said 5.8.4 in the finder...strange) and a pop-up appeared saying it was doing a query all on my Z-Wave devices, which I had never seen before. The text in the window then changed to "Please do not power off/unplug the system or make adjustments to linked/attached devices", etc. That window stays up for a long time, until I get another pop-up prompting me to sign on again with my userid and password. I fill them in and click OK, then get a pop-up saying I need to start a new session and the entire admin console closes.
Signing on with the admin console again, the same thing happens over and over.
I have tried unplugging the eisy and letting it set for a couple minutes; have tried updating the packages again; tried uninstalling the admin console, clearing all Java caches and reinstalling; tried unplugging the PLM, letting it set, then plugging in -- all had the same result.
Clicking on the Programs tab, the list of programs is empty, and I get a pop-up saying
"Could not set file modified timestamp
[./FILES/CONF/DEF/f10]"
"Could not set file modified timestamp
[./FILES/DEF/f1/i1/emap]"
And just like the previous user, none of my Z-Wave devices are working.