Can't create an account on the official bug server, so posting the issue here so hopefully someone can look into it.
I am running a vanilla 1.6.2 client, connecting to a craftbukkit 1.6.2-R0.1 server with no plugins, though I was able to confirm that the bug still appears in the local client as well (at least in creative mode, haven't had a chance to test survival mode.) The bug occurs when you use light for automated farming. In previous versions of the game, turning off the light in a room full of plants causes wheat/potatoes, etc, to immediately (within a couple of seconds) uproot. In version 1.6.2, turning off the light causes the wheat immediately below the light to instantly uproot, but other wheat slowly uproots over time (and in some cases, never uproot.) As a result, light/dark based farming no longer works effectively. Planting seeds in darkness causes the plants near the planted seeds to uproot, but the newly planted seed doesn't uproot. I've been searching for anyone else who has discovered this issue, but haven't found anything related to lightlevel 0 uprooting. 1.5.2 did not have this problem.
I don't believe this is a bug, if you plant crops under a certain light level in 1.6.2 they automatically uproot. It's like trying to grow flowers without any light, it won't work!
The bug isn't planting in the dark, it is turning the lights off after you planted. In version 1.5.2 and earlier, turning off the light resulted in all of the plants uprooting all at once. In version 1.6.2, only the plant under the light uproots, and slowly the other plants uproot, over a very long, long, long time. Not very good when you automate your farm using light.
I am running a vanilla 1.6.2 client, connecting to a craftbukkit 1.6.2-R0.1 server with no plugins, though I was able to confirm that the bug still appears in the local client as well (at least in creative mode, haven't had a chance to test survival mode.) The bug occurs when you use light for automated farming. In previous versions of the game, turning off the light in a room full of plants causes wheat/potatoes, etc, to immediately (within a couple of seconds) uproot. In version 1.6.2, turning off the light causes the wheat immediately below the light to instantly uproot, but other wheat slowly uproots over time (and in some cases, never uproot.) As a result, light/dark based farming no longer works effectively. Planting seeds in darkness causes the plants near the planted seeds to uproot, but the newly planted seed doesn't uproot. I've been searching for anyone else who has discovered this issue, but haven't found anything related to lightlevel 0 uprooting. 1.5.2 did not have this problem.
The bug isn't planting in the dark, it is turning the lights off after you planted. In version 1.5.2 and earlier, turning off the light resulted in all of the plants uprooting all at once. In version 1.6.2, only the plant under the light uproots, and slowly the other plants uproot, over a very long, long, long time. Not very good when you automate your farm using light.
I see that someone has filed a bug report for it in the Mojang bug tracker: MC-30877.