As in exploded or simply razing the buildings and digging underground to make a new base (or rather an extension of the current one).
Bla, in looking around for hints on how to fix the strange issue, I came accross something similar.
http://dev.bukkit.org/server-mods/chdistantfarm-grows-your-plants/tickets/3-crops-in-world-are-not-growing/Edit:
http://dev.bukkit.org/server-mods/chdistantfarm-grows-your-plants/tickets/13-farm-not-growing-at-rate-set/ This one has me thinking that maybe the minecarts are interefering with it? The only problem is that rolling minecarts, like CHdistantfarm, keeps chunks loaded, so I don't know for sure. Only one way to find out for sure.
Heres what I think might be causing it to bug out, I have some cargo carts in the cargo rail floor on the rails themselves, so it's an easy one to test. Fixing this would be easy, just either store the carts+chests when I'm not using them or move the rails down so that the affected chunk isn't also being used by the farm.
Edit: YES! That worked. Now to 'break' it again to confirm for sure that leaving the carts on the tracks is what's doing it.
Edit3: Huh, I can't seem to 'break' it again, so maybe it was just stuck/confused and removing the carts allowed it to get unstuck. In any case, the problem has been solved since the patch I planted has grown, other than a few stubborn ones which haven't quite fully matured.