Thanks for the responses guys. Current status:
I updated the latest drivers for eleven rack and Skype. Still no luck with the microphone working in Skype (it lists the eleven rack as mic input options just like before, but no audio signal comes through when I select line in or any of the other eleven rack options); I also tried setting the microphone to the eleven rack line in from control panel like the other user suggested.
This was tested without pro tools being open; after installing the latest 11R driver pro tools is no longer recognizing the eleven rack hardware and won't open... I think this is because I have Pro Tools LE8. Luckily I backed up my system settings before installing the driver, so I think I have to revert it to that backed up'd state to get pro tools functioning again.
For recording I love the eleven rack, but it seems like a monumental pain in the ass to use it for anything outside of pro tools
After installing these drivers I'm beginning to think you just can't use a microphone connected to the 11R for anything but PT