It sounds a lot like a translation error. libjson interprets the (compiled) entry as “boxed”, which it cannot resolve (probably because it expects an array or an object) to lua.
It probably means that either the mixinto or the final JSON was not properly transported to lua and therefore, whatever you did, is not going to show up. Or, at least, this certain entry is not.
With RP and the console, you could check by running
luas_run PrintTable(radiant.resources.load_json("stonehearth:small_oak_tree")) for example and see what the lua looks like.
Out of interest, what does Jofferson’s current version say? My personal mixintos seemed to work fine, but I haven’t really touched anything too serious.
I could probably squeeze some mixinto stuff into the third position on my list, however…
Edit: Right, I’d have time to take a look if you want me to - I do need to know what you were doing, however. If you could send me your projects (or a very simple test case) then I could have a look. Otherwise, you want to figure out which mixinto exactly is causing the error - and then which part of it.