@fehmi You should not overwrite the stable executables but instead put extract the new versions to Documents/FS-UAE/System as I mentioned in the post. I'm assuming that what happens is that the new version is installed to Documents/FS-UAE/System/FS-UAE-Launcher (as designed) while you are starting the older version extracted somewhere else!
(It may also be a good idea to keep 3.x installed in parallel, for cases where the in-progress-4.x version is not good enough
)