Just if somebody else has a similar problem :)
Firstly I really changed using the right swat+ plus version.
But I also had a differnt problem as well.
In my case the Toolbox hasn't used my tmp files. So it invented the temperature or calculated it from the weather generator.
This changed my water balance and out flow. I had to copy the file from the default into the calibation folder.
And another problem which I caught was that it does not always takes the pointsource/input file which I had in my default project.
Which means, I had to copy ptxyz.txt into my calibartion file so that the toolbox would work with it.
Cheers, Viktoria