A long-standing and unfixable problem in X is that we cannot send a number of keys to clients because their keycode is too high. This doesn't affect any of the normal keys for typing, but a lot of multimedia keys, especially "newly" introduced ones.X has a maximum keycode 255, and "Keycodes lie in the inclusive range [8,255]". The reason for the offset 8 keeps escaping me but it doesn't matter anyway. Effectively, it means that we are limited to 247 keys per keyboard. Now, you may think that this would be enough and thus the limit shouldn't really affect us. And you're right. This post explains why it is a problem nonetheless.
Let's discard any ideas about actually increasing the limit from 8 bit to 32 bit. It's hardwired into too many open-coded structs that this is simply not an option. You'd be breaking every X client out there, so at this point you might as well rewrite the display server and aim for replacing X altogether. Oh wait...
So why aren't 247 keycodes enough? The reason is that large chunks of that range are unused and wasted.
In X, the keymap is an array in the form keysyms[keycode] = some keysym (that's a rather simplified view, look at the output from "xkbcomp -xkb $DISPLAY -" for details). The actual value of the keycode doesn't matter in theory, it's just an index. Of course, that theory only applies when you're looking at one keyboard at a time. We need to ship keymaps that are useful everywhere (see xkeyboard-config) and for that we need some sort of standard. In the olden days this meant every vendor had their own keycodes (see /usr/share/X11/xkb/keycodes) but these days Linux normalizes it to evdev keycodes. So we know that KEY_VOLUMEUP is always 115 and we can hook it up thus to just work out of the box. That however leaves us with huge ranges of unused keycodes because every device is different. My keyboard does not have a CD eject key, but it has volume control keys. I have a key to start a web browser but I don't have a key to start a calculator. Others' keyboards do have those keys though, and they expect those keys to work. So the default keymap needs to map the possible keycodes to the matching keysyms and suddenly our 247 keycodes per keyboard becomes 247 for all keyboards ever made. And that is simply not enough.
To work around this, we'd need locally hardware-adjusted keymaps generated at runtime. After loading the driver we can look at the keys that exist, remap higher keycodes into an unused range and then communicate that to move the keysyms into the newly mapped keycodes. This is...complicated. evdev doesn't know about keymaps. When gnome-settings-daemon applied your user-specific layout, evdev didn't get told about this. GNOME on the other hand has no idea that evdev previously re-mapped higher keycodes. So when g-s-d applies your setting, it may overwrite the remapped keysym with the one from the default keymaps (and evdev won't notice).
As usual, none of this is technically unfixable. You could figure out a protocol extension that drivers can talk to the servers and the clients to notify them of remapped keycodes. This of course needs to be added to evdev, the server, libX11, probably xkbcomp and libxkbcommon and of course to all desktop environments that set they layout. To write the patches you need a deep understanding of XKB which would definitely make your skillset a rare one, probably make you quite employable and possibly put you on the fast track for your nearest mental institution. XKB and happiness don't usually go together, but at least the jackets will keep you warm.
Because of the above, we go with the simple answer: "X can't handle keycodes over 255"