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So I tried putting the seats down and putting the unit flat in the back. This was fine for a few dives but I started having some issues with cell number 2 on the JJ. I noticed that after returning home after a dive cell 2 was very slow to respond compared to the other cells; i put in a small piece of tissue to suck the moisture from the cell and Cell 2 had more moisture inside compared to the other cells. I think this is happening because the position of cell 2 while the JJ is on its back makes it such that all condensation in the head easily drips in to the cell. The cell recovers fully after drying.
So unless i have a faulty cell (month old), laying the unit flat (can side down) is not the way the go!