I've never noticed this either, and I've watched every TNG episode into the ground. I don't own the blu rays of season 3 yet.
Can someone post some good comparison pics?
Here's the early season 3 uniform:
Here's the later one:
It's pretty subtle in SD. The shoulder pads are a little different, and there are multiple seams. Two vertical, and two or three along the side.
The early season 3 uniforms continued to be spandex, which the cast didn't like, so they switched materials (and got rid of the seams).