Your CPU compiles shaders, the GPU runs them. Vulkan shader pre-processing is a form of pre-compiling all the possible shaders your GPU might need before it runs the game (to avoid stutters and freezes later). This is done on the CPU.

I ran into this exact same problem and spent a painfully long week trying to fix it. Unfortunately I couldn't... My only solution was to switch distros and the problem disappeared. I went with Fedora and now every game works like a dream. I still don't know what the issue was but it seems to be something to do with having an AMD system and using steam on Ubuntu.

Probably not the solution you're looking for, but it is a solution!