The horse I ride doesn't like stalls either. Part of her problem is that she's a little herd bound, so she gets herself worked up, unless she's in the barn with a couple horses from her herd. She used to be quite bad, whinying and panicing and has jumped out before. What I did to help was put her in the stall, next to another quiet horse (but not one from her herd) for about half an hour at a time while I did other things around the barn (so I could keep an eye on her). To show her that this is an ok place, I made sure there was always hay and water in there, but also had grain in the feed bin, along with carrots and apple slices in the hay and in rubber feed tubs in the corners. This seemed to work pretty well. It kept her busy for about 20 minutes, and after that she would either start to look longingly out her stall, or munch on some of the hay. I did this everyday for a few weeks, until I could leave her in there by herself for a few hours. She still isn't crazy about the stall. And will occasionally whinny for her herd if she hears another horse whinny, or hears them running around. But she isn't restless like she was before.