I am unable to add the "Yeta Wrench" from Ender IO, the "Wrench" from ExtraUtils2, or the "PA Wrench" from Progressive Automation.

I am using the default configs.

Minecraft Version - 1.9.4
Forge Version - 12.17.0.1937
Mod Version - 1.0-2

It's not a bug, you need to add the items to the config file in the 'whitelisted items' field. You you need to add:
enderio:itemYetaWrench
extrautils2:Wrench
progressiveautomation:wrench

From the description on the curse project page, I'd have thought the Whitelisted Names list would pull in the Yeta Wrench because wrench is listed there.

Is the list case sensitive?

I'm using v1.0-3.