So... a bit more of testing.
Hope it helps and I'm clear enough.
(Otherwise, here's a bunch of random text, haha)
First of all, following linuxares suggestion, I've tried to check my sysmodules.
I didn't mod the Switch myself, but using Hekate Toolbox (v4.0.2) I only see emuiibo, MissionControl and sys-patch as background services.
Tried everything below with ONLY emuiibo enabled.
It really doesn't seem to happen with other homebrew apps -- tested with some functions on DBI, RetroArch (which can't run at all on applet mode) and Checkpoint with these combinations: using both
applet and normal before launching a game and via applet mode while any game is running.
Then I tried using amiigo via applet and normal menus, closing it with the 3 methods CompSciOrBust said: +, Home and the app's Exit button -- but note that with + and Exit I only get to the Homebrew Menu and still have to press Home to go further back anyway.
Still getting the same bug.
Something I noted, though.
In Super Smash Bros. Ultimate and Mario Kart 8, the bug only occurs AFTER usign the amiibo functionality, while in Captain Toad it triggers as soon as the game launches.
Related to that, if I'm already running Captain Toad and use amiigo through applet mode, the function won't work unless I restart the game (this method works with Mario Kart, and it triggers the bug afterwards).
Anyway, as it may be a problem with emuiibo rather than amiigo, sorry for taking your time!