There's an album of the drainage shaft here: http://seekerdarksteel.imgur.com/OCDL5
Hmmm. From your screenshots, I can posit a side-view of this.
T = trap
G = grate
~ = water
| = Wall
f = fishing platform
TTTT
GGGG
~~~~~~~~~~~~~
||||||||||||~
||||||||||||~
||||||||||||~
||||||||||||~
|||||||||||f~
||||||||||||~~~~~
If that's how you set it up, then I think there's some splash from the river. Water levels around waterfalls are ... tricky. I've set myself up for much fun by digging out above a river behind a waterfall, only to have the inside tiles coated in at least 4/7 water.
There's another path which opens up at the bottom of the cliff below the path used for the drainage pit, and that path floods a little bit (maybe 10x3 tiles). But if all of a sudden there were like 10 Z-levels of water at the bottom of the waterfall you'd think that the lower path would flood before the path for the drainage pit.
That depends on positioning.
I forget where the thread was, but water flow in DF is partially pressure-based, but also happens in order.
For example: in real life, water attempting to seek it's own level goes from this
|||||||||||||||||||||
~~~|| ||||| |
~~~|| ||||| |
~~~~~~~~~~~~~~~~~~~~~~~
to this:
|||||||||||||||||||||
~~~|| ||||| |
~~~||~~~~~|||||~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~
to this:
|||||||||||||||||||||
~~~||~~~~~|||||~~~~~|
~~~||~~~~~|||||~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~
That's not how it works in DF. Water seeking its own level in DF goes from this:
|||||||||||||||||||||
~~~|| ||||| |
~~~|| ||||| |
~~~~~~~~~~~~~~~~~~~~~~~
to this:
|||||||||||||||||||||
~~~||~~~~~||||| |
~~~||~~~~~||||| |
~~~~~~~~~~~~~~~~~~~~~~~
to this:
|||||||||||||||||||||
~~~||~~~~~|||||~~~~~|
~~~||~~~~~|||||~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~
Same general effect, but not the one we expect from everyday life.
As to why it's only started now, in 31.05, and not previously? Not sure.
Of course, I could be completely off my rocker, that's not your problem at all, and I've just made an incredibly long and complex post for nothing.
Ah, well.