The empty bars in the screenshot all have whole note / whole bar rests in the full score. As one can see, in the part the bars are empty and are not combined to produce a multi-bar rest.
What might I be missing?
Without seeing the project itself it’s hard to say. Could you zip it up and attach it here, or send it to me by email?
I’ll try by email, the file is to big. (Adding this post just in the unlikely case someone else was curious to see the project and wonder why it isn’t posted here.)