I think it would have been a good idea to take the wheels back to the shop that built them and have them verify the spoke tension when you became concerned about this.
But what's done is done, and assuming you have the spoke tension at an acceptable level now, one thing that comes to mind is whether you stress relieved the spokes. Did you stress relieve the spokes after you re-tensioned them? Here's a link to Sheldon's wheelbuilding article:
http://sheldonbrown.com/wheelbuild.html#seating
Wheels that haven't been properly stress relieved will typically make popping and pinging noises. Is that the type of noise you're hearing?