Flashlight will only be visible when the camera cover is open and once there are too many status icons, you'll have to scroll in order to see the custom ones - but I guess from your first post that your problem is a bit more serious?

Dumb question: Did you reboot lately? I once had a problem with my desktop (couldn't scroll to the others anymore) but after a simple reboot I've never again run into this problem.

If that doesn't/didn't help, you might want to uninstall all the applications messing with the status menu one by one to see whether one of them is the actual culprit.