And if it's not pulling the lever ("q" over the lever, "a"dd a job, "P"ull the lever)... Channels dig down through the floor, so that you're really digging a tunnel with an open ceiling in the level below, not just a shallow ditch. So water in a channel won't actually irrigate the level the channel was dug
from, it irrigates the next level down. I'm not sure, but from the description, this might be the problem. Normally, flood irrigating from a murky pool just means mining up to it, and channeling out only the last connecting wall tile from above to save your miner from learning to swim.
If that is the problem, that's actually salvageable, it just means a little more delay. Mine out (no channeling yet) farming rooms near the channel with a one tile wide passage leading up to it, and floodgate like you did before. From the level above, channel out only the single wall tile left between the water channel and the tunnel connecting to the farm rooms. Your layout should actually be fine in the long run, you can build or mine out stairs up to the empty rooms to use as food storage and possibly kitchen, still and farm workshops. The only extra step would be if you're down into a stone layer for the farms: stone floors irrigate fine but you may want to loo"k" at and "d"ump any loose stones left by mining in stone. Set a zone with I think "i" and have it accept garbage. Preferably near a mason's workshop, and later loo"k" at and un"f"forbid the stones.
I think 2010 underground farms really do need to be irrigated even on soil layers, it must be 40D that doesn't.
edit: or, to have irrigation explained from scratch, scroll down in this thread.
http://www.bay12forums.com/smf/index.php?topic=56914.0