I'm a little confused. MC can not recognise the microphone, it can only recognise the inputs available. Non-USB microphones do not send any "identification data" (USB-mics are also soundcards). So what do you mean "MC recognizes" the mic?
I wonder what you mean by "transporter"? I don't have MC, but I assume in MC the track inputs/outputs are listed in the track header, like in SONAR, not in the transporter, which only includes REC, start, stop, etc. I've never seen inputs shown in transporter (or maybe I've just missed it?). Maybe this is different in MC.
Or do you mean it doesn't show in the level meters? Are you using an interface or the integrated sound card?
Can you record with other methods (using soft synths, guitar etc.)?