I was getting my equipment ready for Dawnguard and noticed that I have a weight capacity of 500 with my base stamina of 500. When I put fortify stamina items on I had a stamina of 640 with the same weight capacity. Is this normal?

I definitely do not recall it working this way. PC User?

http://www.uesp.net/wiki/Skyrim:Stamina

Yes, it's normal.

There is Fortify Carry Weight enchantment if you want to boost your carry weight.