This is related to the upgrade path (via git or via the zip archive). Using git pull or overwriting your install with the latest zip also resets Security.cipherSeed and Security.salt defined in core.php. These settings should not be stored in a file tracked in the git repo, they should be written somewhere else by the app during install. Doing a git pull to upgrade fails because of merge conflicts.

# On branch 1.0.0-beta
# Changes not staged for commit:
#   (use "git add <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#
#   modified:   core.php