You may be sensing a difference between the wheels, but with exception of the tires, it is unlikely that it is any difference in the wheels. Here's a personal anecdote of this: Many people assume that wheels with deep section rims will ride more harshly. But after I got my first set of deep section wheels, my first riding perception of them is that they had a smoother ride than my shallow section wheels. Intellectually, I knew that there really shouldn't be a difference at all. As I wondered about this while riding the deep section wheels, I realized that my new deep wheels were also
quieter than my shallow wheels. My mind had been associating quietness with smoothness, so the smoothness I was experiencing was merely what my subconsciously had been expecting.
Back to the wheel compliance: The vertical stiffness of a variety of wheels has been measured several times, and its been found that wheels typically have stiffnesses in the range of 10,000 - 20,000 lb/in. One of these tests by Josh Poertner at Zipp wheels was already referenced above, and here's
another test that shows vertical wheel stiffness. This means that even large vertical forces result in little wheel compression (compliance). Even at the low end of wheel stiffness, a "hit" that generated a force of 100 lb. on the rider would compress the wheel only about 0.010" - about the same as the the thickness of 2 sheets of paper. This is far less than the compression of handlebar tape, for example, let alone the much larger compression of the tires. The amount of wheel compression is so small, that it is unlikely that a rider could sense this amount of compliance at all, let alone the even smaller difference there might be between two different wheels.
Of course, I'm not the only one who's reached this conclusion. Josh Poertner's experience at Zipp wheels led him the same conclusion, just as it did the engineers and wheel designers at
Nox Composites wheels:
Needless to say, the late Jobst Brandt had already written about this in his seminal book "The bicycle wheel", written over 40 years ago:
There are some people who are convinced that they can feel the difference in vertical compliance between wheels. But its likely those people have never tested this ability in a blinded test (a test where the wheels were hidden from the rider). Those who have tested wheels in blinded tests have found that they couldn't feel differences in wheel compliance (see the reference to the Zipp blind wheel test previously referenced).
(Side note: It's amazing to find how many obvious differences disappear when test subjects are blinded. There is plenty of information available on blind tests of other things, such as wines and violins, but there are a few on bicycle products as well. Here's an interesting one: You'd think that riders would be so sensitive to different saddles that they should easily be able to tell them apart by sitting on them, but in this
blind test of Fizik saddles only half the riders could actually distinguish between two different saddles.)