Probably, the difference between the upper and lower decks is not an exact multiple of foundation height (e.g., they're "seven clicks" apart or something like that.) It could also be that there is too big a gap between the upper and lower decks, if you deleted more than one row of foundation between them.
If you are able to place stairs with cfe on, try placing them, and then re-leveling the upper foundation going from the stairs you just placed, back toward land. Then if the poles poke up, turn cfe off, delete all but the foundation row where the stairs join the two decks, and re-lay the foundation from that row back to land. Turn cfe back off and if you need to, delete the steps, delete the row they were connected to, and then replace that row of upper deck. Then you can place the stairs to shore, and soften the terrain there as needed.
If that doesn't work, you may have to level the shore to be even with the ground under your first row of foundation, before you them raise it six clicks. (What I mean is, after you lay the whole single-level foundation in step one, use the level terrain tool to drag a flat space from the first row under the foundation back onto the shore, so you are starting with a "clean slate" where the ground you raise up in step 3 is sure to start even with the foundation. The lot you are using looks to be very sloped on its way to the water, so the ground you raise up by six clicks may have already been higher than the foundation, which would throw off the height difference,