I don't know if this will help clarify things, or just make them worse -- my apologies if it's the latter.
The only choices that are "remembered" (unless and until you change them again) are the three relating to whether and when auto-generation is done -- when idle, using screensaver, or disabled.
The "Generate now" function is totally independent of those and is a one-time operation. That's just a menu choice, not a setup tick-box option. It works similarly to running a boot-time scan (in Home version, that is) in that you have to select it each time you want to do it.