Hmmm... the next thing I'd do (which you've probably done) is check to make sure the mic is not muted and mic2 is selected (forget where this screen is, but there are 2 checkboxes, mic2 and mic-boost or something).
If all of that is set, not muted, I do not know why it is not working. Does your headphone/mic combo use a SINGLE mini-jack? or is there two (one for mic one for speakers)?
I'm wondering if it's a single connector, is it incompatible with the y-cable (I don't know much about mics through s/pdif).
I'm affraid I am stumped. Hopefully someone who uses their laptop for this will chime in.
I do know that the internal, built-in mic doesn't work with something plugged into the s/pdif port, because I wanted to use it, but need to unplug my digital speakers for it to work.