[TheLastSuperman]

What is your session timeout set to?
Admin CP > Settings > Options > Cookies and HTTP Header Options > Session Timeout

Some sites try to increase that (by daysssss not minutes) and too large of a session timeout setting without a plugin to conteract it can cause issues as you've described. When you prune the session table, granted it reduces the session table from filling up and preventing access however it also resets the user and if they were previously logged in now they aren't and if in a middle of a post and autosave didn't kick in just in time bam now typed post is now gone as well. Be careful with the session table, you can also simply use sql TRUNCATE to wipe the slate clean but same thing will happen i.e. all users still on the site BUT seems as if everyone logged out all at once that way.