Seeds cannot be placed underground, most noticeable when they are placed next to each other.

In SMP, I placed two wheat seeds next to each other in an underground farm. They both immediately popped out of the ground and became seeds again. I experimented with light levels, lining the room with torches and then glowstone, but even lining the walls and ceiling with glowstone did not make the seeds stay planted. Furthermore, when bonemeal was used on the seeds, it didn't work much of the time, and instead also caused the wheat sprouts to break.

The issue was "solved" when I dug out a single block column to the surface above the underground farm, which I would assume implies that wheat currently requires a direct line of light from the sky to grow.

I attempted to recreate the bug in Singleplayer, and had no issue planting seeds underground, even with only one torch (as long as it was in close proximity.)