I assume you're using the "fill holes" function from the edit menu? When you select the edges that you want to fill, they change colour, and the colour gives a clue as to whether filling will be successful. Unfortunately I can't remember the actual colours since I'm at work, but you would expect them all to be the same in the middle of a mesh. Does your mesh have thickness? I think I can see "edges" to the holes. The most likely problem is that there are in fact two vertices very close together at the corner of the holes, not just one. You can combine them, but be careful not to damage your double-sidedness. If that doesn't help, I'll take a look at the AN8 or the OBJ - come back to this thread or IM me.