Is there any specific reason you are keeping her and your gelding apart? I may have understood wrongly, but they are seperated by a fence and each have their own stall without access to the other ones? If there is no bullying or anything like that going on, You said she loves the gelding, maybe take her over to his half one day and see if she will enter his stall. With or without him there. It may smell less "new" and more like horse and especially smell of her buddy. If she goes into his stall then you know it's just a matter of the newness of her stall that's offputting to her. If that works and there is no specific reason to keep her in what is curently "her" half, you could even swop them for a few days. Have your gelding who apparently has no problems with "new" "wear in" the new stall so to speak. Or maybe even leave them together in "his" half for a day or two if they won't fight over food and have him teach her to eat her food in the stall. Again, providing of course that worked, I would put him in "her" halve for a day or two before potentially swopping them back.
Just something I might try to convince her the stall is a good place to be and not a scary place. If nothing else it tells you whether it is just the smell putting her off, or something else.