I noticed this as well, and it really does feel *worse*.
This problem makes Hyper-Warping with my mod Time Control a big problem in low orbit, since with sped-up time you can see the changes to the semi-major axis happening much more quickly (even with zero reduction to the physics engine fixed delta time step). *sometimes* the changes stop completely for maybe a complete orbit or two, but then restart again.
Here's an example - I tracked the vessel's 'orbitalenergy' parameter over time, and it is decreasing. I think you can derive semi-major axis from this value.
At 22:40:57, orbitalenergy was -2528029.48805985
At 22:50:32, orbitalenergy was -2528030.95893785
I think KSP is calculating specific orbital energy using the standard equation as -μ / 2a (where a is the SMA), because my SMA was around 698488.7 m at the start and 698488.3 m at the end. I'm not sure if μ includes your vessel's mass or not. I'm guessing not since the G of the planet is so big it would hardly make any difference.
When I use very high time scales (50x) to speed up time, the vessel's SMA (and orbital energy) loses many meters over the course of a single low orbit. It has to be something screwy with how KSP is calculating the orbital parameters with respect to the planet over time.
I might have to introduce something in my mod where the orbital parameters are captured upon entering hyper warp and 'adjusted' if there are no forces currently acting on the center of mass of the vessel. This can be difficult though given that if I make an adjustment, how do I know the vessel is going to be moved to the 'correct' place... I really don't want to try to figure out how the coordinate system in KSP works so I can basically rewrite the logic that makes a vessel orbit a planet... I guess I could simply ignore the coordinate stuff altogether and use the previous orbital parameters and basic 2-body calcs (which i guess is what on-rails does too).
One thing is for sure, it definitely gets much worse when I use the hyper warp functions of my mod, which mess with Unity Time.timeScale and Time.fixedDeltaTime. I wonder if there's something screwy between the on-rails planets and the vessels happening when I speed time up.