plugin issues

[Connie]

I have a few plugins installed, and I notice that they stay enabled regardless of what I set the plugin to.

For example the dynpages plugins and the php_exec plugin.

please be more exact, which ones?

It is known that the php_exec-plugin can collide, I would not use it
you can use components to add php to your site (and dynpages to integrate them in pages instead of templates)