Is Tsubaki pregnant?
The time skip phase is still a work in progress. A lot of the acts aren't done yet. It's the end of the current main story events.
Yes. If there is still a problem with unlocking Tsubaki's scene than I can check what you're missing.
However, I can't search for vague issues for which I don't know where or for what to look. The story is already at the current end for you in the time skip, which is still a work in progress and has a lot of unfinished acts. So unless you have specific events that don't trigger, I'm not sure what help I could give you.