It looks like a pretty straightforward setup. The tuner should see the guitar if it's plugged into the mic input and it's recognized by the computer (as you say it is).

Try boosting the mic signal input in the advanced options of your sound card mixer to see if a stronger signal makes a difference. Also worth trying as a test if you can is plug a mic into the PC and see if the tuner recognizes a sung or acoustically played note.

Also double check that the pitch range is set properly. I'm not sure how the software is set up by default but usually a guitar tuner would be set up for A 440 as the center frequency range set. Try some other ranges above and below that to see if it makes a difference.