As BetterRed said, Calibre Portable only supports remembering one library.
IMHO the
http://PortableApps.com Dev launcher for calibre is superior, as it makes use of the powerful PortableApps.com framework for portableizing sotware to keep track of the drive letter and update the configuration files (among other things).
Get it here:
http://portableapps.com/node/20518