I don't know the cause of the problem, however I have had very small (i.e. 1/16" +/-) deviations from flat keels in building an AT 17 and an AT 14. The solution, as in the instructions, is to pin the keel to a true board (I use a trued 2X4). Insert a thumb pin or tack from the inside through the seam into the board to hold the keel flat. Then glue the panels, possibly causing a gap as needed, making the keel lie flat on the board.

Be sure to put plastic sheet between the board and the keel so that you don't glue the boat to the board.