You must be in the Navy then. I believe the Army runs 2 miles (for time), the Marines 3 miles, and I think the air force rides a stationary bike(??). When I was in the Marines, and training with Navy guys it always sucked because we'd have to run the course twice, while they went to Mcdonalds on base

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Anyway, I know what you are saying with your knees hurting after a long layoff.
Since you have new shoes, we can eliminate that from the equation.
Is your pain in your knee more of a soreness?? and is it centered on your knee cap area, or off to the side of the knee?? If it is prevalent on the side of a knee, you may have a strained ligament (something I had in boot camp, believe me it hurts like hell to run on) If its just general soreness, I would suggest stretching your legs before and after the run. It helps. Also, have you put on alot of extra weight since you quit running?? Sometimes the body, after a long layoff won't be used to impacting with that much weight on the joints.
Or it just could be a bad treadmill and you have nothing to worry about. That happens sometimes. I have wanted to buy a treadmill for my home, because I can't really run outside in the winter, but I am not buying the cheap $300 treadmill at Walmart, because I think I would break it running on it.