I started a CMS with events tutorial a long time ago. I never finished it but the links and stuff should still work.
[here]
I remember doing a "menu count" where each item on the screen was associated with a number. And when ever you pressed a key it would add or subtract that number, moving the cursor.
But the actual menu was a map that you teleported between with a common event. So there weren't any background events. And mostly everything was parallel process. If it was autorun it erased itself when it was done.
I'd suggest adding a page to those background events with a switch whenever the menu opens thus freezing them. The tricky part would be returning them to the page they were on when you close it. Then you can leave it as Parallel process.
Edit: no, as long as it's the last page in the event, when the switch goes off it'll go back to what ever page was active before. And you only need to do it to moving event's ex: towns people, monsters ect...