They simply dont Spawn, if you take a look at my Previous posting, I did a dungeon and the "Cross way" objects didnt spawn. The Corridors are each made up of 4 Parts thos did spawn without any flaws. But all Rooms that were bigger than 20X20 Blocks didn´t spawn. I had to cut them down to Multiple parts. for them to Spawn.
And if you "Just want some Trees" you can just export them in a older TC version, as I said: Bo3Tools on 1.8 works fine.
But BO3 Bulk Edit can still save you a bit of time. If you have to export Many Objects, you might want to use PlaceHolder for the WorldEdit selection. Bo3Bulk Edit can Remove those from all of your Objects in one go, and remove the "we-" prefix from the file name.