This should be fixed in latest versions.
No idea when this happens. I thought it was caused with some update, but I have the site with 2.2.0 and I had to fix it. Weird thing is that this site was updated 9th May, I added last content 10th May without any problems. No changes, no updating after it and yesterday my plugins were uninstalled. So if this would be caused manual update, it would happen sooner.
An easy fix is to install plugins again but then you will be lost your preferences and they will return to default. Of course, if you remember what you have installed.
Don't go to Menu manager because you lost your menus too then.
The correct fix is:
- go to PhpMyAdmin
- find core preferences plug_installed and copy it somewhere to have a list of installed plugins
Note: you can get this list from admin area too Tools/Database/plug_installed
- then find table prefix_plugins and change installed flag from 0 to 1. Some plugins could be installed (news), some not (pm, featurebox etc). One by one.
This way is everything back.
By the way. It happened on this site too some weeks ago. At that time I installed plugins again. Not sure if I set all prefs back as they were before. Only some days ago I found that I forgot to install PM plugin.