This is getting filed under the truly bizarre category.
I’m working on deploying a masterpage and a page layout as part of a solution package for my current client. I finished designing both files and have added them to my solution. I verified that neither had any of the “extra” markup that SharePoint Designer adds when you create files. I deployed the solution to my environment and everything worked as expected.
I then needed to make a change to the page layout. So, I made the change in the solution and re-deployed the .wsp only to find that my page layout didn’t get updated. I opened up SPD to find that my page layout was marked as “customized”! I checked all of the usual gotchas with regards to this issue (search Google) and even tried to “Revert to Site Definition”. Nothing worked.
I then noticed that Visual Studio had made all of my “<asp:Content>” tags lowercase (<asp:content>). Surely that couldn’t be the issue, right? Wrong. I changed them back to “<asp:Content>” and everything worked as expected.
I guess I should have known better since I’ve had this issue in the past with SharePoint 2007 (http://ericcwebb.com/2011/01/18/sharepoint-page-layouts-extra-markup-added/). However, I at least got an error message with that issue.