This may be a shot in the dark but you could be experiencing what I went through a while back–just a mild case of chromesthesia.
I can remember when I was working on this one track around the clock…I would work and then upload to sc and it would sound like there was all of this stuff missing. I checked cubase, I checked export, I checked player settings, etc…everything appeared to be as it was–understanding that sc has some known degradation issues.
So, what I would recommend, is just taking a bit of a break from the project and then listening to it again when you’ve kind of purged the track from your system.
I still get it, especially if I’m working for extended periods of time, and I’ve just learned to kind of cope with it. But, for me, twice, and after contacting customer support, this was what was going on.