I have same issue.
Same issue for me, and the same workaround of logging in the Windows client which forces the Linux client to logout worked for me.
Hello, can someone confirm this is still an issue with the current stable or beta steam client?
Closing pending feedback.
No longer reproducible for me.
Nothing extracted yet.
I logged in and none of my categories for my Windows games were present. When I logged out (well, I logged back in on my Windows box forcing Linux to log out) and back in later, my categories only then immediately synced to Linux.