It sounds like you have a constant 12VDC being applied to the brake magnets...
Each brake magnet will demand a good 3AMPS DC current if 12VDC is made available to them.. This will burn out your brake magnets if left engaged for long periods of time...
You may have the breakaway switch wired wrong or the key is not plugged in correctly.
If the BRAKE DISCONNECT key is pulled then your trailer battery is providing the 12VDC not the brake controller.
To me this may explain why your #6 setting is now reading 13 verse the 6 you set in earlier. The BRAKE MAGNETs may already have 12VDC on them over riding your #6 setting. Make sure the BRAKE DISCONNECT KEY is inserted good. My keys where keyed in one direction only. You may have forced the key in the wrong direction perhaps... If this turns out to be the case so much time has passed now you may have already run down your good trailer battery...
Same thing applies. If this is left on your brake magnets it may destroy then. It will also drain your trailer battery in a short time frame.
I would disconnect power to the break-away switch from your wiring until you determine what is wrong...
If you have two axles then a total of 12AMPS DC current could be draining down your trailer battery.
Need to get a multimeter and do some measuring of what is happening...
Also some brake controllers do like being connected to the 7-pin cable and have the break-away key pulled at same time. This puts your trailer battery and your truck brake controller electronics in the same circuit and some claim this may do harm to the brake controller electronics...
Just some of my thoughts here - not a BRAKE CONTROLLER expert here. I have used both the P2 Brake Controller and the 2010 FORD OEM built-in brake controller...
There is another quick check thing you can do to determine if the BRAKE MAGNETS have 12VDC power on them. Most of us have our BOY SCOUT compass handy. Mine is in the door pouch haha... You can place this up next to the brake magnet and it will deflect the compass needle rather quick. By now however your trailer batteries could already be drained completely down...
Roy Ken