Not sure if it is something for EnderIO or here, but I'll post it here anyway.
When connecting a redstone conduit to a hidden sneaky lever, it will always submit a redstone signal whatever state the lever is in. It works fine with vanilla redstone.

Sounds like an issue with the redstone conduit, so I would ask the enderio devs. If it turns out to be an issue on my end I will look into fixing it though.

This is a Dark Utilities bug. Ender IO has nothing to do with this.