I am having the exact same problem! I even tried setting an alarm to go off every hour to get myself to stand up and stretch, yet I find myself simply killing the alarm off, and continuing with work.
I guess it is a matter of doing something until it becomes a proper habit. I also have noticed, that it really really helps to have a proper support network. People who will encourage, inspire, and check up on you, to make sure you are sticking to your goals!http://www.youtube.com/watch?v=nKCPcRcJmqc