I believe the
PortableApps.com version of calibrePortable should fix the filenames.
The PortableApps.com approach to making things portable is by saving registry keys etc. to config files and more importantly, by changing paths to compensate for changing mountpoints. It should catch this path too.
Kovid's calibre-portable uses relative paths from the top folder, which doesn't fix filenames, and I have no idea if it makes the adding books folder relative. It probably should, or be fixed to do so, in the event of it being in the Calibre Portable folder tree, in which case Kovid's version, too, should work.