I don't know if this is a similar issue to dokauai's in the forum below.
I've got a multisite setup with subdomains and domain mapping running on WP 3.1.3. I've been using Event Manager for a good few months and it's been fine. Note that I'm only using EM on some sub-sites, not on the mainl site, so it's not network enabled.
After a successful upgrade on a standalone (i.e. non-multisite) install I had a go at this multisite and it's failed.
The upgrade is from EM v3.0.97 to 4.0.6
Initially I got a red banner in the Dashboard saying “Events Manager upgrade not complete, please upgrade to version 3.0.96 or higher first from here first before upgrading to this version. We made a screencast to help you out.”. My events also disappeared from the EM dashboard and from the website - I'm sure they're in the database, but I can't see them.
I then saw your screencast and discovered the database upgrade trigger problem. A de-activate and re-activate of the plugin (at sub-site level) didn't help and the options.php showed dbem_version 3.0.95.
SO...I downgraded to v3.0.98, did the de-activate and re-activate and everything was OK again. I then re-did the upgrade to 4.0.6, followed by a de-activate and re-activate. I'm in a slightly better place: there's no red banner message on the Dashboard, but I still can't see any events.
I've just tried a downgrade to v4.0.4 as you suggested to someone else but I'm still in the same state.
Any thoughts on how to get my events to display again?