I did check in properties and Run is set to Normal Window. I even tried switching it to Maximized once, to see if that would do any good. It didn't. I also check in Winamp options and Always On top is checked.
I also reinstalled the program right on top of the existing one and that made no difference. Then I completely uninstalled Winamp, then reinstalled it, but I still I get the same problem! And like I mentioned, the problem is intermittent.