Calibre Portable (by Kovid) requires the library folder to be inside the portable folder.
Try the PortableApps.com wrapper here:
http://portableapps.com/node/20518
I prefer it since the PortableApps way of portableizing stuff is more robust for little things like this.
Kovid hardcoded a lot of info into the portable wrapper.
The PortableApps Way relies on reconfiguring the appdata where needed, and has solutions in the wrapper for repairing file locations, before calling the main executable.
(IIRC) PortableApps supported multiple libraries from the beginning, Kovid's version only more recently. (More recently than the first time I checked, I know that. That's why I found PortableApps.)