@stokertje – The two items are 100% unrelated, IE the shortcode editor is its own separate package, so disabling one wouldn’t cause issues in the other forms.
As for a plugin caching things in the admin that is a 100% no no. That should never be done simply because of the dynamic nature of the admin, you want the latest info every time you load a page there. So if your plugin is caching the admin, that would be a concern for sure.
If you meant you change the settings and the didn’t show up until cache was cleared, not much we can do about that. The popups are cached with your the pages they are supposed to work on, that is how it should work.
In that case we can’t clear the cache for you as there would be dozens of plugins we would have to check for. Simply clearing your sites cache should suffice though. There is usually a button on the admin bar for Performance or similar, Clear Cache is usually an option.
Hope that helps.