Ahh ... I see the problem. You're using the new betas which do things a little differently.
When you "accept" the template the replacement menu popped up automatically before. Now it doesn't unless it is called from the context menu.
See this video http://www.screencast.com/t/Hyje4Kl2ci
This video shows how to assign a template to a diagnosis so that it appears in the context menu
With the current beta, you can just click on the thin green vertical bar to show the replacement menu ... or use beta 31 which restores this earlier functionality.
Graham Chiu
Beta Downloads and Documentation Wiki
Developer Forum