Regarding the fix oddity:
1st of all, not all pngs are unique. There are thousands of identical pngs in the progetto snaps which act as placeholder snapshots. Same pngs, same checksums, and fix missing looks at several places for a match (rompaths, backupfolders, addpaths, etc).
So it's nothing uncommon that a scan with fixmissing brings you some new files. There are also shared pngs between MAME's titles and neogeo softwarelist for example.
Your setup is not well chosen. Everything in a rompath which is not listed in the datfile is uneeeded. So in your first example if "MAME" is your rompath and you're sanning titles, all but 'titles' will be marked as unneeded (and gets removed) when the belonging options are enabled.
You don't directly run into this because you've disabled the set check....which is also not really recommended.
But anyway, all I can say at the moment is that a plain progetto titles setup with one rompath pointing to a folder where only titles.zip (and if you like the softwarelist zips) are put into works fine. On Windows 10 and on Ubuntu (16.04.1)/Wine (1.6.2).
I've also tried your ini/dat/cmp files on Ubuntu/Wine and it works as expected (screenshot added).
It sounds a bit like another WINE related issue...some versions have really weird sideeffect as you can read in this post...
http://www.emulab.it/forum/index.php?topic=4101.60They resolved their issues by using Wine 1.9.19....my 1.6.2 works fine, too...soo...maybe you can try a new/older wine version.