Hello, and thanks for your report! I can confirm the issue with Protracker 3.15 AGA and Protracker 3.61 too. Do you remember the last AmiKit version in which it worked? Btw. there's nothing in AmiKit update that would break it - except for new Amiberry. Not sure whether Manjaro updates have anything to do with that.
Anyway, to fix the problem, before you start the emulation, disable «Virtual Mouse Driver» in Amiberry/Input settings.
Following are some more details about that feature taken from the AmiKit Quick Guide - Raspberry Tips & Tricks section:
Virtual Mouse Driver in AmiKit enables a smooth experience when switching between Amiga and Linux apps. However, some Amiga programs (like AmiStart, DOpus, Doom and probably others) might not fully register such a mouse pointer. For instance, a DOpus' menu doesn't work correctly if invoked by the right-mouse button over an inactive window. The window under the mouse pointer has to be activated first (with the left mouse button). Anyway, you can always disable Virtual Mouse Driver in Amiberry Input settings. Just bear in mind that it has to be done before the emulation is started (it cannot be toggled on the fly).