Conflict with caching plugin

What is the problem?

With Plugin Organizer activated, caching, minification and remove query strings don’t work correctly.

You need to give more detail. I have no idea what problem you are experiencing. Be very detailed with examples of what is going wrong.

Let me try again..

When Plugin Organizer is activated, it prevents proper caching, minification and removal of query strings from my pages. All three of those things are done with a caching plugin called WP Rocket. I use GTmetrix and it tells me if minification is working, etc. This is when Plugin Organizer is not activated: https://gtmetrix.com/reports/hinescenter.org/8IjuG6IF

When Plugin Organizer is activated it prevents WP Rocket from doing those things.

Is there a certain configuration I need to avoid when using Plugin Organizer with a caching plugin?

When Plugin Organizer is activated it looks like this: https://gtmetrix.com/reports/hinescenter.org/Fx1NSGaI

If that is not descriptive enough, please guide me.
I am using WordPress 3.7.5.

Some caching and minifying plugins combine the css and javascript files on a page load and then serve them up for every page load after that. If your plugins change from one page to the next the caching and minifying must be done for every page load. So that might be your problem. Since you probably have different plugins loading depending on which page is visited the javascript and css changes and has to be minified and cached again.