All issue is in user-dirs.dirs, this is probably due to changes in xdg or something, I know that some package on harmattan's repo contains wrong user-dirs.dirs and that thingy "corrupts" all data.
I would doo clean reflash (with emmc too) and start all over.
Asap ScreenshotMee creates first screenshot in /home/user tracker start making problems. So, it would be nice to checkout user-dirs.dirs before taking any screenshots + to verify path of saved screenshots.