Oh shit, that's one of these questions... I only respond to give you some response, but I don't know the solution. There have been quite a few problems with fullscreen mode, maybe you search the forum for a hint but I doubt you'll find an answer. Milkdrop has aged, and there is not a lot of further development on it.
Maybe this got to do with Direct X ? Do you have DirectX 9 still installed... ? I think the last version was 9.0c, all higher versions starting with 10 are no longer compatible with 9.0c, but can coexist. Which means you can install 9.0c without wiping out newer versions already installed on your machine. Very useful to run older games not compatible with higher versions. But even then, I don't know whether milkdrop would use 9.0c, or rather try to run DirectX 10 in compatible mode. I am not the expert on this.