If I get a notification of changes in reputation, responses, etc, the appropriate column is highlighted on my user page. But they don't get reset unless I select it. So if someone up(or god forbid, down) votes a post I have to navigate to that post from my user page or the notification doesn't get reset. The same is true for accepted answers and inbox notifications. Is it feasible to change this behavior so all the highlighting is reset when the resource is accessed?
If you're talking about the numbers on the tabs on your profile, that is by design. You don't have to clear the counts on the tab. (And they're not "notifications"). This lets you keep track of what's new in an unobtrusive manner. When you visit the tab, the number is cleared, that's it. You need not do some acrobatics by navigating to the post from there--why do you need to? Let the numbers accumulate.
If you're talking about the highlight on the posts not going away, this is a bug.