Thanks for taking a look! I appreciate it.
The first z-level does eat water just like an aquifer, filling to 7/7 and absorbing all water beyond that. However, the interior tiles were all dry stone when dug, so there definitely wasn't any aquifer-like source of water in the process. (Though a wall adjoins the lake.)
Here are screenshots. Ironhand graphics pack.
This is Z-0, the base of the cistern. (Some features torn out for making this test simpler.) The walls are all smoothed or constructed stone, plus a door and a floodgate. The floors are all constructed floors. To the west is part of the pump stack. The bottom of the lake to the south ramps down to feed the pump stack.
I'm certain the walls and floor are solid and no water is leaking to any place on this or lower z-levels.
Z:0 before pumping
Here is Z-level +1. It's just smoothed walls around open space.
Z:+1 before pumping
At Z-level +10 is the top of the pump stack where water flows into the cistern. Pretty straightforward.
Z:+10 before pumping
That's the setup before the pump stack is activated, letting water flow into the cistern. Once the pump is running, Z-level 0 rapidly fills to 7/7 in all tiles:
Z:0 after a little pumping
On Z-level +1, there's lots of falling water. (The pumps are fast enough that there's sometimes 4 columns of falling water coming down.) However, none of the tiles except the ones directly under the falling water ever seem to even reach 1/7 water. Instead, it all instantly vanishes into Z-level 0.
Z:1 after lots of pumping
It really is like some kind of invisible water-destruction-only aquifer that exists despite all smoothed or constructed stone being used in every tile involved.
I tried probing all of the tiles with dfhack (which was quite boring) and none of them had bits.water_table set, or differed in any way other than being in several different biome numbers, but I have little idea what those mean. This point is vaguely at the meeting point of mountain, lake and swamp biomes, but there's 6 different biome numbers reported. Maybe the river is in play somehow too?
Any suggestions about anything else I can do to diagnose it?