CJaysMusic
No offence, but I write software for a living, and have for about 30 years...
No offence, but if it was a bug, everyone would see it and we don't. This fact will tell you that its not a bug and its user error
CJ, chrisby's absolutely correct about bugs that can only be reproduced under specific and/or unusual conditions. Think about the genuine bugs we've seen over the years. Every one of them initially escaped the notice of the programmers, the QA people, and the beta testers. Many were not seen by the first thousand users, either. It's even not unusual for a bug to show up years after a product is deemed "stable", or to affect only 1 out of 50,000 users. It does happen.
That said, it's also human nature to assume a bug when you have no better explanation. We routinely see bug claims on these forums that turn out to be user error, and that happens more often than the discovery of actual bugs. That, chrisby, is the basis for CJ's skepticism. Either of you could be correct, but if we were placing bets I'd side with CJ even though his logic is flawed.
As stated by several responders, the most likely explanation for the OP's issue is a routing problem. In short, what you're hearing is not what you're exporting.
Why do we all presume this explanation? Because we've all made dumb routing mistakes and sat there scratching our heads wondering what was wrong. I've taken 6dB off the master to lower the monitoring volume during overdubs and forgotten to reset it, not noticing the difference until I looked at the exported file. I've inadvertently routed a track or bus directly to the main outs - once only discovering the error after I put a fadeout on the master bus and the tambourine kept on playing.
Junkyard, the first thing I do when troubleshooting this kind of problem is to mute the master bus and verify that everything goes silent. If it doesn't, then something's not going through that bus. If it does, then the next-most-likely problem would be export options. Make sure all the "mix enable" options are checked so that automations are respected, and that "Entire Mix" is selected as the source.