What I did to finally fix it was to change the settings completely on export. The original file was Pro Res Proxy at 1920 x 1080 30fps. I tried to compress it as a reference file then a self contained file with the current settings and then re-compress all frames, self contained with current settings - the Compressor failed everything with the Error -1.
Then I changed the settings to Pro Res HQ 1920 x 1080 30P 29.97fps, re-compress all frames, make a self contained movie. Now with these parameters Compressor is working perfectly.
Seems like there could be a bug in the Pro Res frame rate within Compressor... anyway its working.