That has to do with your framerate, which can't show exactly what you asked for, so it goes for the "next best thing"
I thought it had more to do with how planets and moons are kept in orbit. That was one of the things GA wanted to fix was planets being flung out of orbit at high time steps. US1 had that problem during fast timesteps. In Universe Sandbox 2, its mostly fixed. I remember back in Alpha 8 or 9 you could go up to extremely insane timesteps and the orbits still kept their cool. With the last few updates, you can no longer do that with simulations that have a lot of bodies and objects, it throttles it for some reason.
And because of that, you can't run sims at high timesteps. Ones that have less objects can go REALLY high, but others with dozens/hundreds of objects, it can't. I think it has to do with keeping performance and accuracy of the simulation more then being tied to frame rate. Just imagine trying to calculate dozens of bodies and hundreds of particles at one year per second. That's fast, which may explain why it slows down. Our PC's may not be fast enough to compute speeds that quick, especially for something complex like US2.
I've got a GTX 980 paired with an i7-3770 and get fps into the hundreds (averages 100fps on most sims that are not outragous), and it slows down for me too. I can't get the "Our Solar System" simulation to any faster than 10 years per second before it throttles the timestep.
When the clock icon turns red, it means the simulation is becoming less accurate. The faster you go, less accurate it becomes. The slower, the more accurate. So I assume the game is taking accuracy over speed. I could be wrong though, this is just what I've observed.
A dev will know more about then I do, for obvious reasons of course.