I had the exact same issue today, using the quickstart installation to overwrite all my CB and GJ files....
I had done that quite recently for a FRESH site, so that went smooth as silk, using the Bootstrap Template (FANTASTIC TEMPLATE, btw! Kudos!)
I just crossed my fingers and hoped for the best... as this was a HUGE website I was applying the quickstart to, with TONS of tweaks and language overwrites, etc... but it ALL went GREAT!.... EXCEPT for the GroupJive layout. it was all lined up like Herzen's images.
Wow did I panic.... THANK GOD you guys had this thread! That was all I needed to do, was change the GJ template back to "Default" and BAM... all is good in the world again.
THNX everyone for posting! and for answering! and my not having to cry like a baby with a new thread about my layout problems...
