I think this is a matter of the way the body has learnt responses, and it is difficult to adjust back, especially if you only ride one type of bike/wheel most of the time.
I don’t think this means that one bike is better than the other, but that you have become conditioned to one type. When you go back to a 26er, you’re purhaps either riding it like a 29er, or expecting it to behave like one.
I ride a 26er, but had my first proper go on a 29er last weekend, back to back on the same trail as the 26er. I found the 29er very comfortable, smooth, and grippy and can see how my riding would change to match these characteristics. It also seemed much slower to turn, it caught me out initially. If I only rode that for a long period, I would get used to riding in a way to maximise that bikes characteristics. Because i can maximise the ride on my 26er, I was still faster and enjoyed it more. But it made me quite open minded about different wheelsizes, and gave me the impression that it was less about absolute performance differences, and more about personal preference.
What it did prove though, is that riding lots of different types of bikes and wheel sizes, makes you a better rider. Being an evangelist of just one type will not.