Unless the canvas element itself is being selected - which would be a big oversight on my part, that's the default color palette, which is a blue tint to mimic the Lisa's CRT. Right now, it isn't applied until the settings start loading.
If this is causing any confusion I might put a priority on saving this setting in a way where it can be applied immediately as the page is loaded.
I think you and other commenters are correct - it's just the theming. I can't get it to not have the tint on startup and it goes away when changing the theme as rgovostes described. The reason I was confused was because it starts out as black-and-white and then turns blue, and the blue is basically the same color as selecting text! Oh well, I feel silly now.
Yeah. This is part of why I wanted to get this on places like HN eventually. This is valuable user feedback! For the longest time I kept this project totally secret.
What I'll probably do is serialize the setting data to localstorage so it's available before the system starts up and loads from IndexedDB.
Update: this is done now!