I'm the new owner of a 2006 CLK 500 cabriolet with electric trunk and Keyless Go system installed.
The previous owner has had these issues and I'm attempting to see what's going on and sort them out.

First the Keyless Go ignition works fine however the doors will not open when the fob is near. I have to lock and unlock with the buttons on the fob.
The other issue is the trunk buttons.
When the trunk is open and I push the "close" button on the left it works as it should, the trunk closes but doesn't lock. I have to push the lock button on the fob to lock the trunk.
When the trunk is open and I push the "Lock" button, the trunk starts to come down but then stops and goes back up again.
I found a replacement switch for $15 and figured it was worth a try but it didn't solve the problem so at least I've eliminated the switch as the source of the problem.
Any thoughts?
Is there and sort of sensor on the trunk lid telling it that something is blocking it or something in the way.
It almost seems like when your garage door starts to close and opens back up again because something is blocking the sensor.

Keyless FOB could be an antenna problem in the door, or it could be your cell phone interfering with the signal. Remove your phone or shut it down to test this.