Hello @mastersta, I've transferred this issue over to the steam-for-linux issue tracker because the affected game isn't actually using Proton (or at least it's not supposed to be).
I just put something into orbit on KSP with multiple Proton enabled games installed, no problems here, you sure it's not your drivers that are the problem, they do appear to be older than current, LLVM 6 is not current.
Closing this issue because I can no longer reproduce the issue.
I really think this was a coincidence. They only way this should happen is if Steam somehow caused something with Proton (just a download maybe) to block native. More than likely that would be a hot topic with many people having the problem not just one.
Nothing extracted yet.
Issue: Installing any Windows game via SteamPlay, whitelisted or not, prevents the Linux-native version of Kerbal Space Program from running.
Reproduction Steps:
Logs: See my post on the KSP forums for detailed logs.