According to ForgeModLoader logs, Railcraft doesn't work well with latest Thaumcraft API:

2014-02-02 22:40:44 [SEVERE] [Railcraft] Thaumcraft API error, please update your mods. Error: java.lang.NullPointerException, mods.railcraft.common.plugins.thaumcraft.ThaumcraftPlugin.addItemAspect(ThaumcraftPlugin.java:203)
2014-02-02 22:40:44 [SEVERE] [Railcraft] Thaumcraft API error: ThaumcraftApi is loaded from jar:file:/home/techplanet/mods/Thaumcraft4.0.5b.zip!/thaumcraft/api/ThaumcraftApi.class

I'm using:
Forge Mod Loader version 6.4.49.965
Railcraft_1.6.4-8.3.2.0.jar
Thaumcraft4.0.5b.zip
thaumcraftmobaspects-1.6.X-1e-build2.zip
ThaumicTinkerer-2.1-68.jar

We've only disabled the chunkloading module so far.
Also, I forgot to tell that we're using rcDusts-0.0.6d.zip (among others).
I'll see if I can narrow it down.

Hmm...no that doesn't look like an API error (NPE Exception). Its just being thrown in a section wrapped by the API error catching code.

Best guess, you disable an item in Railcraft and I forgot to add checks for that. I'll add some checks.