Getting unfitter with more exercise

Hi, I've got a problem and I don't seam to understand what it is, I thought I would consult you running professionals before seeing my gp. Here's the story so far: I joined the gym over a year ago, and when I first started I went from no exercise at all, I found I could run for about 10 minutes or so and wouldn't find it that hard to exercise etc, my heart rate would stay about average (for people exercising) I go to the gym about 3 times a week now, but I've found I can't run for longer than 2 minutes. As soon as I hit that time I literally can't breathe and have to stop and my heart rate is so high. Since noticing this I've found running up stairs etc seams to send my heart rate up a lot too. I am not overweight or have a bad diet. I've been trying to lose weight so eat healthy etc. it's getting increasingly more difficult to exercise the more I go and I have been able to perform less and less since joining which makes no sense to me ? Surly the more I go the better stamina I build etc. I was just wondering why this is so ? It's making losing weight so difficult and very unenjoyable due to discomfort when I exercise, and I'm talking really out of breath and pains. Thanks