this is a config "problem". Debug Dosbox has most likely another config and thus is not pointing at a wrong mapper file. Make sure your config point at no mapper file.

Left all "mapperfile=" as blank, seems to have done the trick.

Thanks a lot for the help, everyone 😀 Since this has been an unusual case, there's a slight chance I'll run into a gamepad problem again in the future. I hope not, though.

just remember the one rule, generally you don't need a mapper file. If you have one without needing it, get rid of it 😀

(I dimly remember there being a reported problem with mapper files and joysticks...)

Ok, will keep that in mind 😉

Sorry, I know this thread is old, but I think this is an important issue that many other people may have and I want to express my gratitude to Dominus and mgman for solving it. I, too, had a problem with my joysticks not working in D-Fend anymore (while all of them worked in Windows). I thought I tried everything. It's 02:45am here and I was struggling to stay awake and fix my problem by searching on this forum when I stumbled upon Domino's post about clearing the mapperfile entry. It works ! Well, actually, merely deleting the "mapperfile=" field wasn't enough because the link was regenerated every time D-Fend started up. So I deleted the mapper.map file.
Thank you so much 😘