Hi Nick. I believe the issue specifically questioned in this thread is solved. Several of us at work are running 2018.4 with out any shortcut issues (beyond the usual random loss where you have to restart or re-load your config)
Last I had heard the .4 shortcut issue was fine. I hope I'm not wrong.
Your issue is not completely new though. You might find other threads or other avenues to help fix your problem. Are you sure its just .4? Like is it possible to go to .3 and see if that works fine? and then the moment you go to .4 the problem arises? If so then definitely contact Autodesk about that!
I always save my config after doing any changes at all. Under Customize -> Save Custom UI Scheme I save in to a new folder after every change. So I will have just tons of these folders with configs.
Try setting some stuff up and then saving it out. Then restart max. See if its reset. If so try loading the config and see if it works. Just as a test.
I sometimes wonder if there are permission issues with writing to the files needed to keep the custom setup. Sadly I wouldn't know how to fix this stuff though. The one time I ran in to an issue similar to yours was probably ages ago (like 2008) and i reinstalled 3dsmax completely and I think that fixed it. I recall max just kept losing the shortcuts rapidly and completely.
Wish ya luck.