I have an issue I've seen reported by several other users, which is that the Gcode Viewer runs way ahead of the actual print. It wasn't always this way, it used to stay almost in sync. I tried to fix it with PrintTimeGenius plugin, but that introduced other weird behavior. With that plugin enabled, the print started out way ahead, then it got way behind, then it sped way up at the end.
In trying to troubleshoot, I started disabling other plugins to see if that had any effect. When I disabled the ProgressBasedOntime plugin, the Gcode viewer synced up again with the actual print job. It went from being several layers ahead, to being a second or two ahead, like it used to be.
I'm posting this because I saw several other people with the same problem, saying the viewer was out of sync, but that it was new behavior (had been in sync before). I don't know if this will help them, but none of the fixes I've seen mentioned this particular plugin.
If your viewer is out of sync and you have the ProgressBasedOntime plugin enabled, try disabling it and see if that corrects the problem.
Note: this did cause the "Print Time Left" value to be far less accurate. If that matters more to you, keep that plugin enabled.