Frisco,
The order of the cables being plugged in should not alter the GPS refresh rate. If you are running the latest software version than you are getting the faster GPS refresh rate but not everyone will notice it. Normally we only heard from those that needed low speed GPS information that it was a problem to begin with, so they are predominantly the ones who have noticed the change.
Sounds like you are getting some type of sonar return (blockage) to the right of your transducer. Take some pictures like Chuck said and post them here. Make sure you take one from the left side of the transom looking across the transducer and at the same height as the transducer. Also, see if the line stays there when the boat is drifting or not.