How to hook up my sub correctly.

This is going to sound dumb and I am so please bear with me. The components in question are a pro-ject sub box 50, Pro-ject pre-box rs, and a pro-ject amp box rs. I recently upgraded my pre amp from a Pro-ject pre box ds to a Pro-ject pre box rs. The ds had a sub out rca connection and the rs does not. The sub is powered and has a switch that is either on/auto/off. In the past I set it on auto and when the system is turned on the sub turns on and after off for a few minutes it shuts off. The problem is now that I have wired it using the high level inputs it never auto shuts off even when the amp they are coming from is off. If I unplug the wires from the back of the sub it will but when I plug them back in it auto turns on. Will auto on not work with high level inputs? If I have to use the switch it is ok I just wanted to make sure I am not doing something wrong.