I am using different profiles basically for using different themes at login.
When using another then the default profile, no plugins are enabled (e.g. af_youtube_enabled).
When enabling and reloading settings, they will remain disabled. At some point I also got tt-rss saying, that plugins need to be set with the default profile, but cannot reproduce that at the momentan.
Update: Just noted - in any additional profile, plugins won’t be enabled. When enabling them, things will apply to the default profile, e.g. when not checking all plugins used in default profile, it seems to remove plugins when not checking all… hope this is understandable?