Ninja ripper - problem

Hi, i need your help. I ripped map from GC game (with dolphin). I have tested on 2 wrappers:
1) direct 9 - ripped almost ok, but don't know why are there missing meshes
2) direct 11 - are all meshes, but requires flip normals and don't know why rooms placed on left (in game) are on right, and right rooms on left.

Please help me