I've got a similar problem. Did you figure out what casued this and how to solve it?
Are the files stored in the page files VPP?
No, they are not. It tured out this was the solution; http://world.episerver.com/Modules/Forum/Pages/thread.aspx?id=50577
I've got a page which links to a bunch of PDFs and images stored in the VPP. For a period of time after I publish the page, the files are accessible returning a 200 OK and the content of the file. Then, after an amount of time (which doesn't tie in with any cache settings I can find in IIS or the web.config) the files start returning a 404.
Simply re-publishing the page will reset the cycle, but then after an arbitrary amount of time the files will start 404ing again.