So, you're using the mic to pick up the sound from the speakers to make an audio file? Is that correct? Although from your description I'm still not absolutely sure if you mean the speakers or the mic isn't working.

In either case I would try using a program like Audacity which records directly from the sound card.. it's a much better way of doing what you want... much higher quality sound and it won't pick up external room sounds etc like a mic will.

http://audacity.sourceforge.net/