Gaining Weight While Training?

It just seems like it shouldn't be possible. You have made the commitement to working out. You're getting your 45 minutes of cardio at least three or four times a week. You've added some strength training because you know it's good for you. 

You've gotten better with your overall eating. It's "cleaner" in general. Less processed crap. More real food. Whole grains. Good oil. 

And yet the scale isn't budging. Or maybe, heaven forbid, it's even climbed a couple. 

It can be so frustrating. And so disappointing. 

But don't dispair. We've all been there. I found this article and I love what it says. It references running, but the principles apply to whatever workout you do. 

http://www.bioendurance.com/blog/i-trained-all-summer-for-the-marathon-and-havent-lost-a-pound.htm

I really believe that losing weight is MUCH MORE about how you eat than how you exercise. What is your experience?