With Salamander 2.52, I got the usual (but confusing) "Computing Differences" in the caption, immediate results, and after a few seconds the caption said: More than 32 768 differences.
With 2.53 preview build 38, I got this frightening message:
Insufficient memory to allocate 891352880 bytes. Try to release some memory (e.g. close some running application) and click Retry. If it does not help, you can click Ignore to pass memory allocation error to this application or click Abort to terminate this application.
Can this be avoided, perhaps with the 'slower' method as a fallback?

I would really like to be able to compare large binary files...

When I swap the files, it takes a little longer before the error occurs, but it still does, with the same (largest) number, and without showing any differences.
I use Windows Vista x64, with 4Gb physical memory. Is it running out of address space?