I am having problems with cleaner 6 photo-jpeg contrast levels. Stripping away all optional filters and checkboxes, leaving Cleaner 6 with just the Photo-jpeg original settings, I see a notable difference in contrast levels and image detail compared to Quicktime
This is most likely due to your source being a different color formar than the Photo-JPEG codec. P-JPEG at 76% and above is a 4:4:4 codec. Below it is 4:2:2. If your source is YUV 4:1:1, 4:2:0, 3:1:1, or RGB, then it is possible that Cleaner is just doing a bad job of converting it. If you are using Mac OS X 10.4, then you can just use automater to batch a bunch of exports using QT.