This is so annoying it feels like it’s a bug, but someone must have felt like it’s a good idea…it’s not! When You try and render several midi clips that are on one track and if some of those clips are muted…well if you render that track to one event then all the muted stuff magically becomes unmuted and included. Bad call! Please fix this.
I was unable to reproduce the behavior. So some investigation is in order, with an eye to to ruling out elements to help find the culprit.
First thing to do is start up with Cubase safe start. if you can reproduce the issue, continue reading.
Is it tied to high asio load, or asio load irrelevant?
Does it happen regardless of the mix of track types in the project, or can you narrow it down to a specific track type?
Same thing for plugins.