Yeah I am almost sure that's the reason too, and from yesterday. But it means I need some cps2 decryption code to be able to compare the roms to see if their only difference is really this region byte, and if there is more than that then keep the region clones, it's very possible I'll be obliged to re-insert a few of them and not just one. The code in mame doesn't look too hard to port, but I have other things in my mind, so it might take a little time.
Anyway good news for the 1st report : it's actually some very old bug, it dates from the time when I started to add neogeo games on top of neoraine using the code for neocd ! There is a part I totally forgot for the initialization of the game because the width of neocd/neogeo games can be either 304 or 320, until now all neogeo games had a width of 304, which is the default, and which is obviously wrong for some of them, like here for samsho2 ! It's just a stupid bug, the big surprise is that it took us so long to notice it !
Here is a screenshot with it fixed