Got an small update in the meanwhile:

- So I've switched the cables on the motors with each other, does not seem to make anny diffrence. So I asume the stepper-driver settings are equal, otherwise results should have been switched too I suppose.
- I've measured the coils on both of the stepper motors. results were equal.
- I had 2 diffrent colors (so probably 2 diffrent types too) of filament, white on E0 and yellow on E1. When I switched the filament rolls on the extruder, problem seemed reversed. So I thought maybe it's something about filament density.
- I took a new spool of filament and tested it on both of the extruders. Then the problem and difference was similar again, E1 feeding slightly more then E0.

So looks like I'm back to the start again...