I think I got what was happening. From the video I recorded you can see there is only one Neo Geo MVS entry in every view but when I deleted it in the launchbox ui I found another one that was probably generated from the mame set and I didn't noticed before. Essentially when I have imported a second set of roms with the same name of an existing set this new set hidden the original one in LB e LB next. But in big box was the original set that hidden the new one. Don't know if this is a bug, for sure I was made something strange but I think that hiding one or the other depending on the version of LB/BB is confusing, the set should be merged o displayed twice (evend with the same name), or even just display a warning to make the situation more clear.
However in the end is resolved deleting the set I imported in LB (so the last one, not the one from mame) and reimporting it with totally a new name (Neo Geo Overclocked) and doing this everything work. I have just a question, when I go in manage platforms now I see my new platform (Neo Geo Overclocked), the scrape as combo value is used only for scraping and not for other king of aggregation at UI level right? I'm asking because I'm using the UI in italian and since in Italian there is not a direct translation for "scraping" in this context, the translated word in my UI is a bit generic (just to give you an idea translating it back from italian to english it can be done as "bind to").