Thanks for letting me know. I forgot to forward the -u flag to the proper places if more than 1 file was being resized on a multi-core CPU.
Please re-download the tool, it should be fixed now. (You should of course use double quotes, but you probably do, because it would not have worked otherwise.)
photoresize.exe -w200 -u -r -q85 "-cC:\MyDestination\<PATH><NAME>.JPG" C:\MySource