After saying you may be out of luck, here's something I've found: Image Forensics Search System
Apologies for cropping your post but I didn't want to fill the page. I got quite excited when I saw this so downloaded it and gave it a pretty thorough test drive today.
So, firstly it's pretty old. The website only mentions OSs up to XP and the installer looks old. It also requires JRE but, I just used Uniextract to extract the IFSS installer which includes a java folder and it seemed (at first - more on that shortly) to run fine like that without JRE on my PC. I'm guessing though that this also means that the included java version is pretty ancient.
Anyway. I randomly picked a folder of 103 photos of my local town, picked one out and created a selection of edits of it... I mirrored it, shrank it to a 75x56 thumbnail, grayscaled it, graffitied it, and rotated it through 90 degrees.
The program is easy enough to use, a nice simple layout and interface. You just load your initial pic, select a few options (some of which I still don't understand entirely...) then point it to the directory you want to search and let it go.
It's pretty slow. Took around 5 minutes to scan the 103 pics in the target directory, and while it's working javaw.exe is taking about 90-95% of cpu cycles which also means that the program itself is more or less unresponsive while working. I mostly had to use task manager if I wanted to cancel a search.
Results-wise through, it's great. It picked up on all the edits I'd made with the exception of the 90 degree rotation, though to be fair I think most duplicate finders fail on that too with the exception of Visipics.
It's different in its approach. When you select the target directory the program scans this and loads it into a window from which you can then select which pictures you want for comparison. Select all is the useful default, but this part of the process itself takes ages... two or three minutes for my 103 photos.
Then when it's finished, it doesn't show you a list of "hits" but lists all the files in the target directory, sorted hierarchically according to percentage match.
So far so good, but onto the main problem... I went on to try it on a folder of about 5,400 downloaded pictures, and five times it just exited itself after a few minutes for no apparent reason, before it had even loaded the folder. I even made a copy of the folder and renamed all the pics in it, thinking it might be an issue with path lengths (you know what long names downloaded pics can have...) but that didn't help. I then put aside my non-install version and ran the installer properly, but that made no difference.
So, mixed results really. I'm just running it now on a directory of 934 National Geographic photos and it seems to be fine with that (Edit - completed successfully). If I can find some definite cut-off point beyond which the program won't work, then I think it's definitely a keeper - depite its slowness and cpu-hogging java, it's still the only program of its type that I know of.
Interestingly, even when I ran the installer it still creates a java directory in the program folder rather than actually installing java. Not sure what to make of that.
Ultimately I guess, a better solution is if we could hunt down a duplicate finder that has the option to only show cross-directory matches, e.g. show when a pic in Folder A matches a pic in Folder B, but not when a pic in Folder B matches a pic in Folder B. I've been looking through various programs today but none of them seem to do this.