Sometimes its an issue that both panels join with a edge. When wiring together, one panel might 'snap' over the other one. We had relaxed the situation by taking away the top of the edge with a plane. Just a little bit as indicated by the red lines on the attached (lousy) drawing. This helped a lot especially at the joint between floor and side panels.
I can't remember we had an issue at the joint between keelson and floor panels; at least not a step of 1/8". Are you building from kit as we did?
On page 61 the manual says, that the bottom panels will lift off the cradle when wiring things together. In case you fixed the floor panels to the cradle prior wiring: That could make a difference maybe?
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