Unrelated to your skype problem, but on your Linux PC, if you're using ALSA with an HD-audio chipset be sure to read Documentation/sound/alsa/HD-Audio-Models.txt in the kernel sources, you might need to specify the model/jacks configuration for your motherboard in order for all ports to function. Also try everything in alsamixer from a shell prompt because it can be tricky to get the proper input going.

If you're not using hda then I dunno

I don't use Skype so I can't help with that one, sorry.