Here's a screenshot with the overlays:
https://runeapps.org/i/dmqfe
You can see the purple box is missing the puzzle box. The green box looks like what it incorrectly thinks is the entire window overlay. Upon startup, there is a red box around the entire window, so it is finding the whole window, but the overlays aren't.
Analysis of the clues, AFK alerts, and XP meter work great, so the targeting seems to be okay, but the overlays are wrong.
Alt1 Toolkit version: 1.5.6
Browser (Chromium): 83.0.4103.106
Image Acceleration: AVX256