Ok I found two culprits for my issues:
1. I usually make sure I use the USB ports on the motherboard for this kind of stuff. Turns out, since it's USB 3.0, it actually gave Windows trouble detecting the DFU device. Plugging in to a front USB port (which are USB 2 and connected straight to a USB 2 header on the motherboard) helped with DFU detection.
2. The latest of the recommended "rockbox with patches" version caused the USB drive detection issue (version rockbox-with-patches-a010b7cM-130217.zip )
The versions which allowed my iPod to be detected were:
-fallback rockbox version
-previous patched rockbox version rockbox-with-patches-93130beM-130110.zip
So in this case I recommend not following the instructions on the first page and avoiding the latest patched version, and going with the emCore build or the older patched version.
Edited by zephyr90 - 2/27/13 at 1:14pm