Thank you @kalusha
I was able to install and activate all your plugins excluding these ones:
adrotate
newsletter-extensions
newsletter-wpusers
real-cookie-banner-pro
wpdm-advanced-custom-fields
wpdm-daily-download
wpdm-extended-shortcodes
wpdm-lazy-download
wpdm-tinymce-button
wpdm-watermark
Anyway, I already have some suspects about the plugin Health Check & Troubleshooting. As I see when you activate the Troubleshooting mode it writes the file health-check-troubleshooting-mode.php to the folder wp-content/mu-plugins. Inside that file at line 237 there is a line of code that updates the WordPress core option “active_plugins”. This is the option that stores the set of active plugins.
FDP never saves that option. In my opinion, this is the core territory, and no plugin should save it. But FDP filters that option to specifically disable plugins. If the file mentioned above saves that option before FDP removes all its filters, then you have the issue that you reported.
This issue doesn’t happen for standard plugins that save that option because the code FDP runs before any standard plugin, and it removes its filters before the first standard plugin. But I’m afraid in this case the file written by Health Check & Troubleshooting saves that option before FDP removes its filters.
Have you activated the Troubleshooting mode and then visited a page where you had some plugins disabled by FDP?
Are you able to repeat the same steps to reproduce the same issue?
If so, can you do it with and without Health Check & Troubleshooting active?
I suggest you clone your website to a staging environment if not done yet. So you can do all the tests without risking anything with the live site.
Until now I wasn’t able to reproduce the same issue, but I will investigate deeper on my testing installation.
Have. great day!
Jose