I believe I have the same null pointer exception crashing my server, and I believe it has to do with the top 'target' slot of the EE condenser being empty. I think it's using "net.minecraft.server.ItemStack.doMaterialsMatch" to check whether the thing it's about to pull for the wood pipe is the same as the thing in the top slot, and if it isn't, check the next stack in the box. But when there's nothing in the top slot... Well, there's no code to handle that case, seemingly. Boom, NPE.
In my case, I'd just emptied this condenser, moved it, placed the BC wood pipe, RS engine, torch, threw some crap to be condensed in the box, and then the server blew up before I could place the target item.
Edit: Also, my world was fixed by: http://forums.technicpack.net/index.php/topic,5663.msg38697.html#msg38697
HTH
- Hrocdol