Whilst I agree it isn't perfect, I don't think there is anything wrong with have your 'Move-up', 'Move-Down' buttons there - a lot of desktop applications follow a very similar pattern to the UI concerned with manipulating list-boxes.
A more aesthetically pleasing technique would be to allow your user to drag-and-drop the items within the listbox, but when dealing with winforms this would require a fair amount of GDI++ custom control programming to get it so that it was both functional and fluid.
If I were you I would move the buttons so they less floaty, and keep them inline with the top right of the control.
Something this like this is a good example to keep it neat and tidy:
