The same issue occurs in Nintendont, I was thinking if this could be useful to figure out why it happens in Nintendont.You're looking at the dolphin compatibility. Dolphin is an emulator and has no bearing on the same compatibility standards as nintendont since nintendont is not emulating.
Try looking at the wiki.gbatemp list for nintendont; http://wiki.gbatemp.net/wiki/Nintendont_Compatibility_List