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Ubuntu uses a different encryption technology to encrypt the home directory (ecryptfs) whereas Fedora has whole-disc encryption. With ecryptfs, only data inside a filesystem (or directory) get encrypted (ala windows xp pro) leaving Filesystem stucture data exposed.
Whole-disk encryption (aka LUKS) (as the name suggests) encrypts the entire filesystem, leaving a malicious HDD thief unable to distinguish data from random noise, or even to see how much data may be on the hdd. With ecryptfs, on ubuntu, your user password is your key, and thus by logging in, you unlock your home directory. With LUKS, it is possible to create a key, put it on a USB flash drive and use that to automagically decrypt the volume.