The yogurt you buy in the store has thickeners added to it, something you are not doing when you make yogurt at home.
Do you know how warm your yogurt maker gets? When I make yogurt, I use a Coleman personal sized cooler, filled with hot tap water (about 120 degrees Fahrenheit). I make a gallon of yogurt, heating the milk to 180-185 degrees, then cooling on the counter until it comes down to 110-115 degrees. Then I add the culture (I've re-cultured for about 8 months now and it is still really good yogurt). I make culture a pint at a time, removing the cultured milk to a pint jar, well sealed, and put it in the Coleman along with the gallon jar. I add about a cup of sugar and a half teaspoon of real vanilla extract before sealing the jar up again. I leave it in the cooler for 8 hours. I've found that more time than that results in a tangier yogurt.
You might just try shortening the time in the yogurt maker to see if you are culturing it for too long. Also make sure that the culture you are using is kept well covered and in a very cold part of your fridge to keep it from degrading or getting contaminated.
Good luck and let us know your progress.