I have the same issue with the saved colours disappearing after quitting the app.
M2 Mac mini w/ MacOS 15.6
Version 25.07.4 (ca0459d8)
Python 3.13.5 Qt 6.9.1 Chromium 122
nb; Not sure why I’m still on v25.07.4 (the ones above show 25.07.5). I install from homebrew and it says the latest version is already installed.