OK, two possible issues here. Issue one you say your roms are zipped, but in your first image above you do not have the checkbox to unzip games checked. Two even if that is checked, i'm gonna assume there is more than one file inside the zips, which in that case Launchbox has no idea which file is the file the emulator needs so it just picks one, seemingly correctly sometimes, and incorrectly others.
My advice, never keep roms zipped, especially roms that are more than one file, it will cause you more headaches than the minuscule amount of space you are saving by doing so, i'm assuming inside the zip is a bin and a cue file, there is no need to compress them, and you may even find it beneficial to convert them to another format like CHD, which is one file and is also compressed, but Retroarch cores can read it as is, no decompression needed.