I realize it is a mod interaction between Mekanism and Thaumcraft that is probably unintended.

In addition, Aura nodes do not keep their aspects when moved, either; they seem to totally regenerate when unboxed, creating a new aura node. For example, I could box a fading aura node with only terra, and get a bright node with 3 different aspects on it.

I'm disabling cardboard boxes on my server regardless (simply moving them with something as cheap as a cardboard box is probably OP).

Crash report: http://pastebin.com/CpCK54qi

Just add an entry for aura nodes into the box blacklist file :)

I am having approximately zero success in adding anything except stone (the example you give) to the black list. I've tried "blockAiry:0", "Thaumcraft:blockAiry:0", and "tile.blockAiry:0" and all of them tell me that the entry couldn't be parsed. So, how do I do this?

Edit: Okay, not parsed. It wasn't parsing a blank line in the file.

Here's what it says (repeat x10, since I have 11 items in the blacklist, and one works, which was "mob_spawner:0"):
[19:17:15] [Client thread/ERROR] [Mekanism/Mekanism]: BoxBlacklist.txt: Couldn't find specified block on line 5