I had the same issue. For some reason the upload_extra_script.py is different than what’s on the official, so replacing it fixed the problem for me.
To save you (and anyone else who finds this thread) the problems of compiling it themselves, just see attached 
There’s two versions. One is the default with the Y axis to the back (how TT has it) and the second is with it to the front.
Just unzip the file, choose the one you want, throw it onto the Micro SD card in the SKR and you should be good to go
TT-Skr-1.3-Precompiled.zip (225 KB)