I'm not sure if this is a bug with Akashic Tome or Thaumcraft, so I'm reporting it in both places.

Mod list here

With both mods installed, only the Thaumonomicon is able to be added to Akashic Tome, and all other books become Entropy Crystals, regardless of what mod they're from, or in what order they were added. This happens even if the Thaumonomicon isn't even added to it.

Azanor/thaumcraft-beta#742

I found this issue today but only happened adding tomes using thaumcraft "arcane workbench" and broken up all my normal entropy crystals rendering them useless for crafting.
I think original poster added the thaumonomicon to akashic tome before building the arcane workbench for progression reasons, and then using that workbench for all other book adds triggering the bug each time.
Still i think it's an akashic tome issue and ocasionally unaware players could fall into this problem if not fixed or somehow making it impossible to add tomes in arcane workbench interface.
And though i didn't dabbled on it too much, it could mean some unwanted book to crystal exploit for using in some recipes that dont need the special workbench.

Honestly, I had forgotten this issue was still open, but I haven't revisited it in over a year, so I'm going to close it. I've mostly moved away from Minecraft, and I have no idea if this is even still valid.