This question has been asked numerous times so I’ve created an FAQ for it on the FAQ page for Plugin Organizer at https://www.jsterup.com/dev/wordpress/plugins/plugin-organizer/faq/. Your situation would fall under the second example. It is happening because of the way the cache is built and the fact that the caching plugin relies on the same plugins being loaded on every page.
Q. Can Plugin Organizer be used with caching plugins?
A. The simple answer. Yes. But you must understand how your caching plugin and Plugin Organizer do what they do. If your caching plugin creates a minified version of the javascript files loaded on a page then there is the potential that Plugin Organizer will cause the caching plugin to constantly recreate the minified javascript files.
Let’s say you have plugins A, B, C, and D active on your site and D is disabled globally. All 4 plugins add javascript to the site. On https://www.yourdomainnameyouuse.com/post-1/ you have plugin B disabled with Plugin Organizer. On https://www.yourdomainnameyouuse.com/post-2/ you have nothing disabled by Plugin Organizer and plugin D has been enabled, overriding the global setting. When someone visits https://www.yourdomainnameyouuse.com/post-1/ a minified javascript file has to be generated containing the scripts for plugins A and C. Then someone visits https://www.yourdomainnameyouuse.com/post-2/. The minified javascript file has to be recreated because the javascript for plugins A, B, C, and D need to be loaded. Then someone visits https://www.yourdomainnameyouuse.com/post-3/ and the minified javascript file has to be created again because the file has to contain the scripts for plugins A, B, and C but not D.
The above example explains how load time and caching can be affected with a caching plugin that creates minified javascript files. It basically renders the caching plugin useless.
Another example would be a caching plugin that creates a static version of pieces of the page. Again lets say we have the same plugins and the same posts. When someone visits https://www.yourdomainnameyouuse.com/post-1/ static pages are created with the content from plugins A and C. This cache has a lifetime of 300 seconds for example. When someone visits https://www.yourdomainnameyouuse.com/post-2/ it has the content for plugins A and C but it is missing Plugins B and D because the cache hasn’t expired. This can cause unexpected content and errors.
There are different ways that caching plugins work and they can work together with Plugin Organizer. These are only 2 examples to give an idea. But you have to understand how they work and how you are affecting your cache by disabling plugins.
