(Triaging old bugs.) The current version of the manual clarifies that this is intended default behavior, though it can be changed through a preference:
"When running with the fastcheck preference set to true—the default on Unix systems—Unison uses file modtimes for a quick first pass to tell which files have definitely not changed; then, for each file that might have changed, it computes a fingerprint of the file's contents and compares it against the last-synchronized contents." Users who have programs that routinely update files without updating the modtime probably need to set fastcheck to false, which will avoid accidentally missing such files, at the expense of slower synchronization. I believe that's uncommon on Unix, which is the reason for the default. -- Mark J. Nelson Anadrome Research http://www.kmjn.org