Yes, VMWare makes the icon disappear. It *SHOULD* come back when you quit VMWare, though.
As for changing the partition name, the easiest way to do it is from within Windows, rather than the Mac OS. When you have Windows up and running, open "My Computer' (Or just plain "Computer" if you're in Vista,) then click on the hard drive (drive "C",) and hit the F2 button. (If you're on a notebook keyboard, you'll have to hit "Fn-F2".) That will tell Windows you want to rename the currently selected icon. (You can also right-click on it and choose "Rename",) then just type in your new name.
Please note that Windows partition names are *NOT* case sensitive to the Mac OS, so you can't have a name like "Windows HD", it will appear as just "WINDOWS HD" to the Mac OS.