Compiling Courier MS

I am posting this here, because I am not sure where else it would go…
Yesterday, I complied a 60K word manuscript and exported using the preconfigured Courier manuscript, and I am trying to sort out if the problem occurred when I compiled it or after it was edited using ProWriting Aid. Initially, the text was fine for chapter 1, but then the other 26 chapters were compiled in chapter 2 which went from double spaced to single with a few paragraphs appearing much much smaller than the size 12.
Another copy which I complied was left flush and attempting to indent a paragraph-moved the whole page.

I am usually able to figure this sort of thing out, but this one has me baffled.

An easy check to see where the problem is would be to compile to another format, like PDF. If the problem still exists, it’s not Pro Writing Aid’s fault.