Category links not working

I’m working on a custom theme and while mostly everything works fine, I’m having trouble with my category links. I have an horizontal custom menu at the top of my template and it displays the links correctly, but when I click on a category, it still displays the posts for all categories. For example, when I click in cat1 it still displays posts from cat2, cat3 and so on. I have all plugins disabled and it works fine on twenty ten. Can anyone lend a hand please? I’d post an url but I’m on a firewalled localhost. Thanks in advance.