The problem

When Global Configuration Cache is enabled, plugins are stuck in the state recorded at the time of cache creation, meaning that a plugin that's been enabled will stay enabled until cache expires. Manually disabling or enabling a plugin should also refresh the cache so that this operation completes successfuly.

How to reproduce

This is a little tricky to reproduce but here are the steps

Prerequisites

• Go to Extensions > Plugin Manager and make sure System - Debug is published.
• Go to Global Configuration and make sure Cache Handler is set to File and Cache is set to OFF - Caching disabled.

Testing

• Go to Global Configuration > System and set Debug System to Yes. Save your current configuration - you should now see the debug output at the bottom.
• Go to Extensions > Plugin Manager and unpublish the System - Debug plugin. Debug output no longer shows. Publish it again. Debug output shows as expected.
• Go to Global Configuration > System and set Cache to ON - Conservative caching. Save your current configuration - debug output is still at the bottom.
• Go to Extensions > Plugin Manager and unpublish the System - Debug plugin. Debug output still shows - this means that the plugin still runs even though it should not.

The solution

During my tests I've found out that cache for com_plugins is stored in the cache folder as well as in administrator/cache. My solution would be to clean both of these by adjusting cleanCache() in the administrator/components/com_plugins/models/plugin.php model, but I'm open to other suggestions. Personally I'd like that we'd keep caching for system objects such as plugins in only one place (let's say on the administrator side).