I JUST found out what was wrong with it... Nyerguds had mentioned that in the N64 C&C the only 3 usable houses are Neutral, GDI and NOD so anything set to team 'SPECIAL' won't show up so i am now looking at the map in the map editor and seeing a refinery in the GDI base that was not there when i played it on the N64 but it was because it's team was set to Special, it's an easy fix i guess what i'll do than is just change it's team to GDI or Neutral
EDIT: I love the 'Replace' Function in notepad. i've just replaced all Special own stuff to GDI and i'm going to insert it into my official work in progress alternative N64 Rom mod i'm working on, not yet sure what level it's going to be yet, perhaps i'll put it in the place of nod level 11 or 12, im about to make the 3d terrain for it, ill upload it and show you when i'm done