For some reason big trees leaves decay right after generation, using 2.4.14 and Spigot 1088.

The big trees are being removed from Minecraft 1.7, so this issue can surely be closed when 1.7 is out.

But could you please answer the above question?

Are we talking about a BO2/BO3 or the normal BigTree in the Tree resource?

If it's a BO2/3 the leave blocks most likely have their decay bit set. You can fix this by only using the 0-3 data values for leaves.

if it is a normal big tree, could you please test with normal CraftBukkit? TC just calls Minecraft's internal tree place method, maybe Spigot has done something to that method, or maybe it was MC 1.6.2.

Inactive.