PublishPress affects WP site even when deactivated?

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I’ve been trying out the PP Capabilities plugin, and have found that my WP site doesn’t work as expected even after deactivating the plugin.

E.g. I can allow a contributor to upload media, and they still have this ability when the plugin is deactivated. Also the same goes for them to be prevented from editing their published posts.

Does this mean PP is affecting something in my database so the changes are still reflected whether or not the plugin is active?

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