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I had made a couple of changes to a site which I believe caused this issue. The symptom is, click on 'View all site content' on a subsite and it will show the view all site content page of the root site. I made some changes to the master page:

                                <td class="s4-titlelogo">
                                    <SharePoint:SPLinkButton runat="server" NavigateUrl="/" id="onetidProjectPropertyTitleGraphic">
                                        <SharePoint:SiteLogoImage name="onetidHeadbnnr0" id="onetidHeadbnnr2" LogoImageUrl="/_layouts/images/siteIcon.png" runat="server"/>
                                <td class="s4-titletext">
                                    <h1 name="onetidProjectPropertyTitle">
                                        <asp:ContentPlaceHolder id="PlaceHolderSiteName" runat="server">
                                            <SharePoint:SPLinkButton runat="server" NavigateUrl="/" id="onetidProjectPropertyTitle"><SharePoint:ProjectProperty Property="Title" runat="server" /></SharePoint:SPLinkButton>

with the NavigateURL set to "/" for the titlelogo and titletext. I realised I probably only wanted it to be the titlelogo and applied the master page and reset subsites to use it.

I subsequently changed the masterpage page but problem exists. As a side thing we changed the default AAMs for the site so that was the other change made.

When I try go to a subsite and directly change its master page I can browse its library for example:


but when I try check out an item I get a File not found error:

The URL 'parents/_catalogs/masterpage/v4.master' is invalid.  It may refer to a nonexistent file or folder, or refer to a valid file or folder that is not in the current Web. 

So I assume my attempts to reapply the master page have failed for the subsite.

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After further investigation I can't seem to change the master page for any subsite, for example from /parents/_Layouts/ChangeSiteMasterPage.aspx page I alter it to a different master page and it changes it for the root site collection. All the subsites remain unchanged. – pigeon Jan 29 '12 at 2:28
I have faced this and it had its root into Alternate Access Mapping and host header used while creating the web application. – Ashish Patel Jan 29 '12 at 3:43
I've still got the original AAMs for the site, but haven't checked to see if the issue exists when accessing it using that URL. Or was the problem due to the fact I had altered the default AAMs with the master page referencing the '/' root site for those links perhaps? – pigeon Jan 29 '12 at 5:45
up vote 1 down vote accepted

turned out to be Alternate Access Mappings at fault here. I setup an Internet zone and it fixed the links. As you mentioned Ashish, the host header and bindings need to be in place when creating the web application. The alternative fix was to Extend the web application with the correct bindings and host header information. I was able to change it without having to do that.

Thanks for putting me on the right track.

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