Tente usar o caractere de escape para o arquivo de lote:
ffmpeg -y -r 20 -i %~d1%~p1%~n1.mkv -vf ^"drawtext=text='Watermark Text':x=10:y=H-th-10:fontfile=/Windows/Fonts/Calibri.ttf:fontsize=45:[email protected]: x=(w-text_w)/2: y=(h-text_h)/2^" -c:v libx264 -preset ultrafast -b:v 1000k %~d1%~p1%~n1