What Linux distro (and release) are you using? Only Ubuntu is supported, last time I updated it was strictly Ubuntu 22.04 LTS that was required for building app images, then the resulting app image could then work on almost any modern distro. I may need to update this to make it work on Ubuntu 24.04 LTS since GameMaker has moved on a bit with the most recent Ubuntu support.
I tried it on KDE neon recently which is a linux distro nearly identical to Kubuntu and it worked with both a Wayland and an X11 session. The only difference between the two distros is KDE neon is strictly based on Ubuntu LTS releases and it has newer KDE software releases than Kubuntu does. I'm not sure why you are having issues. KDE neon also doesn't use snap packages by default even though Kubuntu does, but that should be unrelated to the problem as well.