And one more longshot....something you THINK is routed to a physical output just MIGHT actually be feeding a bus with the same name. I know that sounds convoluted, but I had it happen to me where everything sounded fine on playback, but the bounced mix was missing several parts. It turned out that my routing had gained a bus with the same name as my main output
I deleted that bus path from the IO setup and reset those track outputs properly and all was good.