Transparency in Zelda 2 majora's mask

Hey Guys,

I'm trying to play zelda 2 and most things are running well, but trees and certain borders are transparant or semi- transparent such as the stumps you jump across at the very start of the game.

I'm running the newest version with jabo's plugin, I tried rice's but it looked like a scene from an 80s arcade game.

system is 2.8Ghz, 512 DDR with a 64 mg nvidia card

Any help would be great thanks!