Check the MasterPageFile property is being set correctly and you could set any master page from gallery e.g. MasterPageFile="~site/_catalogs/masterpage/v4.master".
example usage in a Page layout:
<%@ Page Language="C#" Inherits="Microsoft.SharePoint.WebPartPages.WikiEditPage" MasterPageFile="~site/_catalogs/masterpage/v4.master" meta:webpartpageexpansion="full" meta:progid=”SharePoint.WebPartPage.Document" %>
Update:
There are different ways you can refer the master page in your page layouts:
- This is a relative or absolute path to a master page. Relative
locations are based on the page instance's location - i.e.
"../_catalogs/masterpage/custom.master" will find custom.master in the
current SPWeb's master page gallery, which may or may not be the
top-level site's master page gallery.
- Site-Relative Master Page
~site/_catalogs/masterpage/custom.master.
- Site Collection-Relative Master Page
~sitecollection/_catalogs/masterpage/custom.master.