torproject version: 5.0.3 (based on Mozilla Firefox 38.3.0)
portable apps is 41.0.2
Both, concurrently on MS XP.
As far as I know, both claim they won't interact with the other.
Can you verify, or otherwise comment, on the following:
Starting 41.0.2-portable after the torproject's firefox is running yield a message that there is another version of firefox running. 41.0.2-portable needs that other version closed before it can run. Reversing the start order, that is starting torproject's firefox after 41.0.2-portable is running, seem to work. Although I do suspect that there are still some bad interaction.
Since in the 1st order, that is 41.0.2-portable after torproject's firefox, 41.0.2-portable didn't start, I haven't disabled the addons I have for 41.0.2-portable before trying. It is apparent that torproject's firefox uses the, perhaps modified, noScript addon. I use it for 41.0.2-portable too.