I had the same issue, and it took me about a month to figure out the solution. You can find a post about it here:
www.beckybertram.com/.../index.php
Basically, I created my page layout in SharePoint Designer, and then copied and pasted it into Visual Studio. When I deployed the page, though, it was behaving like you've explained, like it was customized. I finally checked the page using the SharePoint API and it was indeed registering as customized. This totally baffeled me, because SharePoint thought that page had been customized, even though the feature had just been activated and it had been no where near SharePoint since I had activated the feature that deployed the files to the Site Collection Master Page Gallery.
It turns out the culpurit was this: SharePoint Designer put these two tags in the Page Directive at the top of the page:
meta:webpartpageexpansion="full" meta:progid="SharePoint.WebPartPage.Document"
when I originally created the page in SharePoint Deisgner. For whatever reason, when a Page layout gets loaded and it sees these directives, it logs that page as being customized. So, when I copied my markup from SharePoint into the Page Layout in Visual Studio, it took these meta tags with it, and when I activated my feature, SharePoint said, "Aha, these pages have been in SharePoint Designer" (which they were, originally, just not since I had deployed the feature), "... they must have been modified!"
I'm not sure if this is the issue you're having, but it certainly tripped me up for a while