I believe this probably is not jockey's fault but rather nvidia-current,
based on the contents of the file (seen from dupe bug 981048):
$ cat nvidia-current-updates_hybrid.conf
# This file was installed by nvidia-current-updates
# Do not edit this file manually
blacklist nouveau
blacklist lbm-nouveau
alias nouveau off
alias lbm-nouveau off
prevents nouveau from working and as such the system cannot boot
** Also affects: nvidia-graphics-drivers (Ubuntu)
Importance: Undecided
Status: New
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https://bugs.launchpad.net/bugs/956091
Title:
Jockey does not remove 'nouveau' driver blacklist when deactivating
nvidia driver
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