This isn't something we know about, actually. Update 21 shouldn't have changed anything related to performance. I also am not able to reproduce this just by running any simulation for that long.
You said you saw it when running the default sim and Jupiter was ejected. I wonder if the issue is related to Jupiter continuing farther and farther out. Do you see the slowdown consistently in that scenario, or with any other sims?
Just to confirm, the Jupiter that was ejected was an added object that was 'launched' toward the sun with auto-velocity, orthogonal to the ecliptic. After accomplishing many eccentric orbits, each more so than the last, it finally escaped.
This had the apparent affect of dramatically slowing down the game... What is odd is my CPU usage remained constant at around 25 percent or so amongst the cores. If I remember correctly, prior to this update with Vsync OFF my CPU usage could be fairly high depending on simulator demand; and with Vsync ON, CPU usage was at a steady 20 ish percent. It's as if something is limiting the CPU resource or bottlenecking the sim as a confounding body is introduced to the standard solar system sim.
My GPU's usage is difficult to figure out as well, occasionally jumping to 50 percent usage at near max clock, but typically hanging around 5 percent downclocked. Something has definitely changed for me though.
I'll do some more testing to see if I can reproduce the situation in other sims. Having my attracting bodies being reduced by 35 percent merely by adding a single rogue planet isn't a good development though.