hm... I guess you have set the background option to var(--joplin-background-color2), right?
I can confirm this behavior. The background can be updated by opening the settings menu.
Also changing the theme via the preferred light theme option, updates the background directly.
I can see that in case the system theme was updated the handled css variable --joplin-background-color2 is not updated. So this should be addressed to the app devs I guess.