You need to find out where the water is coming from.
The new windows are much tighter than what you had before. If you had old windows with storm windows before, you may have had frost on the storm windows. This is because the moisture in your house was getting past your old interior windows and was stoped at the storms. With the new, better insulated replacement windows, the moisture is now blocked at the inside of your house and if is cold enough outside, you will get condensation on these windows.
The best way to determine how much water you have in your house is by useing a sling sycromiter, (probably not spelled right).
Your contactor should be able to have his supplier perform this test.
Remember, windows do not make water but, windows can be the first sign that you have too much in your house. Think about how much water your couch must have!