Did you update both TWLMenu++ and nds-bootstrap?Before I get too deep into chasing the issue, does the AP patch feature work for you on Mario vs DK Mini-Land Mayhem (USA)?
I have everything apparently set up correctly but I still get the issue reported in the compatibility list. I also noticed that the AP_FIX_PATH field in the nds-bootstrap.ini file is blank after I force-close the game, so I think it may not be writing it in the first place. Writing it by hand before launch did not work for me either.
Also, if you're referring to the glitched sprites, that's not caused by AP.