Especially happens when you first open the crafting grid and put something in, seems to get more stable the more you do with it.
Putting arcane stone blocks from thaumcraft into slots will alternate between

<Thaumcraft:blockCosmeticSolid:7>
<Thaumcraft:blockCosmeticSolid>

Void nuggets alternate between

<Thaumcraft:itemNugget:7>
<ore:nuggetVoid>

I also noticed that occasionally, when saving the recipe, it will cut off part of the tag.
For example <StevesFactoryManager:BlockCableName> would turn into <StevesFactoryManager:BlockCable>. Occasionally even the closing bracket goes missing.
I haven't been able to reproduce the cutoff issue since the first couple recipes I tested.

Ok, the ":x" is metadata, and could be weird mod behavior, but the cutting of of tags is really weird.