From Dr. Mirkin’s eZine:
Asking people to stand at work, rather than sit, is not good advice because standing-without-moving is no better than sitting, and will make you too tired to exercise vigorously when you are finished working. If you are a vigorous exerciser, standing all day will slow your recovery from your exercise program.
The highly-publicized studies that showed sitting is harmful for exercisers were flawed because they failed to separate casual exercisers from vigorous exercisers. No one has shown that standing up instead of sitting confers any special health benefits, and standing without moving around can cause additional problems such as varicose veins and swollen feet. Contracting muscles circulate extra blood to strengthen your heart and draw sugar from the bloodstream to lower high blood sugar levels. This does not happen when you just stand in one position without moving your muscles
I am not completely convinced, but I think he raises a good point about the failure of the study to consider individual differences in fitness as a confounding variable.