this should be very much independent of the source file, however i created such a source file (using a 3rdparty encoder because ffastrans cannot do it) and set the prores encoder just like in your image. With the result that everything worked fine except my target file shows framerate 29970/1000, not sure if thats a bug from mediainfo or it really is that way.
However, i was not able to get to the same error messate as you show, what ffastrans version are you using?
What also worked for me is instead of choosing the framerate from the dropdown in the processor, i used a populate vars processor and set %s_somevariable% to 30000/1001. Then i used %s_somevariable% as the framerate in the prores encoder. In this case, my output file showed exactly this framerate instead of 29970/1000.
