have you tried restarting the web publishing engine itself via command line? That doesn't require you to reboot the database engine and kick off your other filemaker users.
FMSADMIN RESTART WPE
in the terminal app.
As for the errors, do your users disconnect properly or are they closing out the tabs? I've been tracking an error that I believe is caused by "orphaned" sessions that clog up the RAM cache and eventually cause a memory leak.
Also, how many concurrent connections do you run and what is the hardware of your mac mini? I've found that more and more, the mac mini just isn't the right hardware for webdirect. Most webdirect configs recommend a quad core processor, which none of the mac minis have.
Thanks, I will check to see if there is a "log off" button. For the moment, maybe only 1-2 users on each database at a times.
I have not tried the web publishing restart, will try next time,
You can add a button to your solution that uses the exit application script step that will allow them to log off gracefully.