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as said, you've been confused (well, i said deceived) by jackdbus which has been bundled into jack2, and much to great dismay for all the people that don't give a sh*t to pulseaudio to start with...

in general you tell apart jack1 from jack2 by package name and/or version numbers: jack1 versions are currently tagged as 0.12x.x, while jack2 versions are like 1.9.x .

the ~/.jackdrc fiie is NOT a settings nor configuration file whatsoever--its role is for plain jackd auto-start feature ie. the one that gets executed when some jack client application runs and the jack-server is not currently up and running at the time.

problem with many jack2+jackdbus installations is that people fail to understand that the ~/.jackdrc file is ONLY meaningful to jackd alone; once you get jackdbus into the scene that file is baloney! it won't serve any purpose nor, better said this way, no single part of the jack-audio-connection-kit software will ever read nor write to it. nuff said.

from the moment you have jackdbus rigged into the system, it just takes full control and charge of the jack-server auto-starting and what not. also, running jackd on those environments is simply a masochistic and futile experience: you'll get only pain on every other run; mind you, if you want to have control of the jack-server from the command line, then use `jack_control` as your best bet.

hth.
cheers