I've had Terranigma crash when transitioning to the overworld and FFIII(US) crashes on the title screen.
Both of these rom images worked prior to updating.
Maybe someone can contact this guy "SiENcE" regarding the work he's done to the snes9x dingux port he's been adding to? He has Rudra No Hihou working now.
http://crankgaming.blogspot.com/2010/03/snes9x-139ff-ver20100313-for-dingux.html