I've never tried installing calibre Portable on an encrypted drive, but I do know I wouldn't trust the bloatware they bundle on those drives. I usually delete it, but if I wanted to encrypt my drive I would use something like
TrueCrypt.
TrueCrypt is an excellent piece of software, notwithstanding that the developer disappeared and tried to scare users away in suspicious circumstances. And the independent security audit, pending a final review, has been
completed and passed.