I am having the same issue as here New Force.com IDE (Eclipse) - not auto-deploying?, except the solution chosen isn't working.
I have Build Automatically checked and I've also already selected "Work Online" for the entire project. These two actions are the only solutions made available under the above link. Nevertheless, every time I save the project, nothing saves to the production environment unless I manually go into each component and select "save to server" under the Force.com IDE menu item for that component. I'm using Kepler 2 as well and the latest Force.com IDE Plugin.
I'm able to get the Sandbox Project I have to auto-deploy, just not in production. I can also roll out new changes to the classes/vf pages via the changesets successfully (i.e., my test classes are working)
Please help, this is so annoying.