Group Policy not applying

Here is the scenerio:
I do have all the users in the same OU, and the computers are in different OU. I want to apply the Group Policies on the computer OU. When I put both the users and computers in the same OU, the policy applies fine. But, if the user is not on the same OU as in the computer, the policy doesn’t take effect. The policy I was trying to test with is just a simple IE default home page, in the user configuration section. I tried disabling the unused portion “computer configuration”, the result is the same.
Am I missing something very obvious about the Group Policy application? Putting both the computer and the user in the same OU is not an option here. I would appreciate if somebody can help me on this.
Thanks.