Printer changing print head after changing offset

First of the printer used is a K8400 with two E3D v6 Print heads.

The problem I’m having is when trying to change the X and Y offset in Repetier Host for either Extruder-1 or Extruder-2.
When i set the correct offset and started a test print. Had Print Head-1 become Print Head-2, and Print Head-2 had become Print Head 1.

The issue happens sometimes, but other settings that may be 0.1mm in a different direction becomes normal again.
My solution have been to switch the offset settings of Extruder-1 and Extruder-2, but that solution stopped working on the settings on the correct offset.

I’m pretty sure it isn’t the E3D Print Heads that are the problem, other than it having a different length between them.
And i have tried finding a setting that switches them, but i haven’t found anything.

So i would be nice if somebody had a solution?

This is a marlin problem. If you have for example nozzle two active before you start a print and the gcode is made for nozzle one but does not make an explicit toolswitch in the code you can have that problem. The workaround is to make sure the correct nozzle (one that will be used first) is the active nozzle (manually).