Knee Issues

I know this has been addressed on the boards already but my knee pain/condition doesn't seem to be as severe.

On week 2 of c25k and LOVE it, but my left knee...Ouchie. Not horrible pain, not swollen just generally uncomfortable. I haven't taken any kind of otc meds and have to be honest, haven't been stretching properly before or after. (I know I know I'm on Santas naughty list). When do I need to be super concerned? Is discomfort normal since I'm not stretching and starting such a high impact sport? I walked very very very regularly prior to starting this and didn't have any knee issues. Also, do I need to use better shoes maybe? I'm currently using New Balance Trail Running shoes. Hubby thinks that alternating heat and ice may help. Thanks everyone for the tips.