I have just amended line 255 so it reads:
$new_dir = $filedir . "/" . $imgadjust;
As a result, new cropped files are saved into the same master folder "crop", "proportion" etc.. rather than creating a new folder to hold each image which means I don't need to worry about the default permission problem on new folders. All seems to be working fine but please let me know if anyone sees a problem with this fix.