It seems general enough. I don't think this oddity has anything directly to do with the DD mod, but i could be mistaken. I will reference this post from there.
Anyway, i got an axe.
When you chop down the tree, the nearest farmer rushes over and 'plants seeds'.
But no seed turns up from the plot, it is still inside, and the farmer does not carry a seed.
There is no plot still left under the tree, but chopping it down seems to 'free' the seed.
The soil seems 'prepped', for finalizing the planting process. All a dwarf has to do it to walk over to the plot that the seed is lost in, and generate a planted square using the 'plant seeds' job.
The square they plant in, isn't the square where the tree stood. Where the tree stood, there is only soil, no farm.
I'm going to have to go with my guess that somehow a tree grew in a planted plot, dislodged the plant from the plot but didn't dislodge the seed from the plot since there was a tree there.
Luckily, you can fix it by either freeing up the planted square by chopping down the tree, or dismantling the plot itself. The first will not dump the seed, but allow the seed to be planted somewhere else in the plot, while the other will just dump the seed like when dismantlig a building.
In fact, i just realized. The seed DOES show up with the 'l'ook command!
It's lying inside the plot, in a specific square! But it is not tagged as a [ B ]uilding material like planted seeds. It's more like just lying there like any other free item in any other shop. This is why it wasnt shown by loo'k'. Dwarves try to find it since it should be readily available, but is in fact blocked by a tree.
Sometimes items get stuck in workshops inpassable squares as well. I guess thats from either throwings or deconstructing shock-full workshops that cause items to spill out into surrounding squares. This is much the same thing.
I think half the problem is that either the plot when designed 'cut into' the tree, or that the tree later grew up into the plot. Since the seed was found inside the tree as well as the plot, i guess it grew there.
In any case, even though we cannot see it, i think that the plot square under the tree is counted as 'farm'. The tree probably grew and overwrote, not replaced, the current square's contents. The plot does not show up, but it should still exist.
When chopping down the tree, i think that the engine 'replaces' the current floor, which finally kills off the plot, and forces the seed to change location. The new location is where the dwarves go to finalize planting. If the farm square was destroyed when the tree grew, one would have expected the seed to change position by itself, seeing as it did when the tree was cut down.
It is a fact that the engine replaces floors that are no longer visible. I use constructions that make the floor invisible(such as walls, trees should also work the same) to clean away mud and cluster stone residue from my floors. If you get some of those yellow/blue patches on your floor, just slap on a construction, remove it, and bam you have an awesome clean floor.
Either the former floor data is over-written, or any superficial features are removed, such as coloured floor residue from mining cluster stones, mud, or maybe a farm plot.