I've been working on a similar but unrelated issue - in my case, I'm gathering all of the textures for a scene along with the scene file into itself, organizing it into it's own project directory, and putting it into a ZIP file.
While my MEL script was working great to do all this, every time I unpacked the file and tried to open the scene, it couldn't find the textures, because they all had full paths back to their original locations.
One would think you could just reset the .ftn attributes on the texture nodes to relative pathnames (i.e. "textures/somefile.tif"), but what I found was if I did this, Maya immediately re-translated it into an absolute pathname and stuffed that into the .ftn attribute - ack!
After inspecting some other .ma files that worked the way I wanted, I eventually discovered that if you use a full path to the texture file, but with a double '/' to seperate the part of the path that's the project, from the part that is the texture filename, it will automatically repath them when you open the scene in a new project location.
So for example, I would set my texture filenames to something like: "c:/path/to/my/project//textures/somefile.tif", and when I opened this scene from another directory location it all worked great, the parts before the // would get retranslated by maya into the location of my new project.
I don't see anything anywhere that documents this behavior, has anyone else seen a similar type of issue, or is this a known "feature"? This turned out to make my problem of moving scenes (with textures intact) from one computer to another a lot harder than I expected.
--Coop