kdiff3 Version 0.9.98 (64 bit) on Mac OS El Capitan.
When all conflicts are resolved, I click the save button but it remains enabled and clickable. Only when I click one of the "next difference" buttons the save button is disabled.
The real problem though, is that sometimes the changes are not saved to the file, whichs is specially painful on long merges.
Invalid bug, not problem of kDiff, but problem of SourceTree