If you ever find yourself missing a scroll bar on the web part properties panel (The panel that pops up on the right when you select edit web part) – then your most likely culprit (and fix) is MSO_ContentDiv.
Simply Add: <div id=”MSO_ContentDiv” runat=”server”> around PlaceHolderMain in all master pages used.
Likewise, if you are having strange alignment issues with your web part properties panel, this should help to fix it.
