The main reason I sold my Fractal Audio FM3 and got a Stage was because of the pretty unacceptable lag between switching scenes and channels, which are supposed to be instant according to Fractal. I wonder if something is up with your Stage specifically because I am also extremely picky about switching lag, and I have never noticed any lag on a Stage. I don't think the clock sync error has anything to do with switching at all. It just means you have to enter the date every time you power the thing up (which is also super annoying, I also had that issue and got a replacement from Kemper).
I already did get a replacement for the clock error so I agree that's it's not that.