When creating a Master Page for your SharePoint site, you need to add the placeholder for your future or current Page Layouts. Most people use the Minimal Master Page that can be found throughout the internet, some from Microsoft and from others who have made their own.
The problem with a lot of the popular Minimal Master Pages is that they do not have ALL of the needed parts. Specifically the proper way to include the Page Layout place holder.
If you use the minimal code along with your valid CSS/HTML you may find that your Web Part property page cutting off from the bottom when in Edit Mode of your publishing page. The “OK Cancel Apply” bottom row will seem to disappear.
One solution is to wrap the required “id=”MSO_ContentDiv“” place holder in a table cell with a “class=’ms-bodyareacell’“.
<Placeholder id=”MSO_ContentDiv” runat=”server”>
<table id=”MSO_ContentTable” width=100% height=”100%” border=”0″ cellspacing=”0″ cellpadding=”0″ class=”ms-propertysheet”>
<tr>
<td class=’ms-bodyareaframe’ valign=”top” height=”100%”>
<A name=”mainContent”></A>
ContentPlaceHolder id=”PlaceHolderPageDescription” runat=”server”/>
ContentPlaceHolder id=”PlaceHolderMain” runat=”server”>
ContentPlaceHolder>
</td>
</tr>
</table>
</Placeholder>
</td>
Another option is to use a <DIV> to wrap the content area while eliminating some additional formatted cells.
<A name=”mainContent”></A>
<!– Page Description –>
ContentPlaceHolder id=”PlaceHolderPageDescription” runat=”server”/>
<!– Main content area –>
<asp:ContentPlaceHolder id=”PlaceHolderMain” runat=”server”>
</asp:ContentPlaceHolder>
</div>
Source: Mike Smith’s Tech Training Notes
I chose option one as I built my first SP Master Page to have my full Property Pane to show.