This happens to me too in VS 2008. I've lost many controls because of this issue.
Many times, I haven't realized it moved the Location of my controls until its too late - and I've already saved. I believe this can also happen when I'm in code-view, while the designer is open. So I can constantly be saving my code, but it will also be saving the Design, and I can't see if its screwed up or not.
Very frustrating. Here's the workaround I've used so far: never add controls directly to the Form/UserControl. Put everything inside a Panel-type container, and it will only move that one Panel. So you can simply readjust the Panel Location, and all your controls will be back.
Does anyone have a real fix for this issue?
Ryan