wheat seeds unplant themselves and occasionally others that are in the vicinity of other seeds or directly next to other planted seeds. I have this problem in both Vanilla single player and the latest Feed The Beast version.

The dirt is also always next to or near water so that cant be the issue either, the ground also stays plowed. they seeds just do not want to stay planted and i dont have this problem with watermelon or pumpkins (at least not yet)

Just try planting some seeds in survival mode in massive plots of lands/ a large number of seeds at once to potentially see the same thing happen to you.