Tried to smelt Chaos Ore from Silent's gems, and as soon as I try to put it in the furnace this happens:
http://pastebin.com/Yse9d1yp

Also happens with Thaumcraft's native clusters.

Running
Alt-F4-1.8.9-0.0.2.4
forge-1.8.9-11.15.0.1697-universal

Edit: Also trying to use alumentium from Thaumcraft broke things as well.
http://pastebin.com/Nz4Yuwp4

Double Edit: Trying to smelt with Coal and make smooth stone crashes as well.
http://pastebin.com/s21vpdNU

https://drive.google.com/file/d/0B0mCmvEcGbUUeDRJM20tQ3BRM00/view?usp=sharing
this should be it I think.

Sorry, can you test with the latest version http://minecraft.curseforge.com/projects/alt-f4/files/2275418 and then tell me what happens when you try to do the same thing as you did in the initial crash?
As well, tell my if you can see the registered recipes in JEI?
Really I need a log that has information from when you start up a world, as that's when the recipe registry list is filled.

will do,it will be a little while though. work unfortunately

Can I get your full log?, things don't break for me with any of these items, but there is a chance that the recipe registry copying failed, because it's trying to reference a blank arraylist.

You mean my full startup log or something else?

Yes please, it'll contain information that might tell me why the recipe arraylist is empty

Looks like it's all fixed. Possibly had the wrong version on the server as well. So I see everything/nothing crashes me now. Sorry for the hassle!