You're not imagining it, yes they do run smoother! Back in Postwar days when operation on O31 was the norm, locos had at most ONE traction tire. MPC-era diesels had two traction tires on the same side of the truck, which was still ok (see analysis in the next paragraph.) But putting tires on opposite sides of the same axle is a modern-era thing. You might get away with it on O72, but for sharp curves it's a devil's bargain to increase pulling power at the expense of smoothness and realism.
On sharp curves such as O42 and below, the curved path traced by the outside rail is noticeably longer than that of the inside rail. Each set of wheels on the locomotive is rigidly connected to the axle. So when the loco enters a curve, to accommodate this difference in length, one or both wheels have to skid. Rubber tires on both sides of the same axle inhibit this from happening. So momentarily, perhaps a couple of times per second while the loco is navigating a sharp curve, there's a sudden increase in friction. This can cause the loco to slow down or stall. As you've already surmised, this is most noticeable when you're running the loco by itself. When you're pulling a train, the sudden increase in friction is masked by the drag and momentum of the train. But when you're pulling the loco out of the engine house and it suddenly enters a sharp curve, it will lurch and hesitate, destroying any illusion of realism.
I'm not sure why your center wheel shifts more in one direction than the other. That's the axle with the main drive gear. You might check the side-to-side play, and the free play in the driving rods. You're fortunate that your Hudson is designed to be "convertible." Another benefit of using the non-tired wheel is better ground electrical pickup. I despise rubber tires. For the reasons above and others not mentioned here, I would remove them from every loco I own, if it were easy to do so!
