This has been happening to me constantly and it's super annoying... For example, right this second I'm editing "Teitoku no Ketsudan"(Japan) for Sega Genesis which is "P.T.O.: Pacific Theater of Operations"(USA). Both names are completely different but the Japanese version keeps having its Japanese box art overwritten and changed to the USA box art. No matter how many times I delete/replace it , as soon as I click "OK", it gets overwritten by the USA boxart. I can sometimes workaround the issue by messing with the name a bit, for example, if I name it "Teitoku no Ketsudan " (with an extra space at the end), the box art sometimes works just as expected at least until I refresh that games meta data. This happens to me constantly, I even tried removing all the images for all languages of one game and they kept coming back! Ended up deleting them from the images folder manually and then everything appeared to work as expected for a previous game but I'm tired of doing that because it happens so often and even my workaround doesn't always work... And I've tried refreshing meta data which was suggested before but that seemed to exacerbate the problem.
I'll try to share some screenshots when I run into this again.
tl;dr: launchbox should NOT override images set manually by the user period. At most, it can add secondary images which it sometimes does correctly.