Just got a horse from the stable outside Whiterun, but it doesnt appear if I fast travel to Whiterun. However if I fast travel to Riverwood the horse appears next to me. Anyone have any clue what the deal is or is it a bug?

Have you checked the stables? I believe I read somewhere, that when you fast travel to a city your horse goes to the local stable.

Hmm no havent checked yet. Just strange how it will appear at that one town, but not the other when I fast travel.

When ever I fast travel my horse is always ourside the city gates, either at the gate or at the stable.

When you fast travel to Whiterun, you are placed inside the city, so how could it appear next to you? It'll be at the stables outside. When you fast travel to an open area in the world, it will be next to you, or you'll be riding it, depending on whether you fast traveled while on/off it. Riverwood is an open town.