issues when going to www vs not going to www

I'm working on my dev box and noticing that I'm having issues when I go to www.host.com vs host.com.

Specifically, I had a javascript hover effect that isn't being applied when I go to www.host.com however it works when i go to host.com.

My thoughts are that its a problem with the server and when I merge to live it will resolve itself however I am not quite sure if thats really the solution.

Has anyone ever experienced this and what should I do?