The Section1 and Section2 files are new to the book. Ever since I added them, both Chapter 1 (ch01.fm) and Chapter 2 (ch02.fm) generate/update as Chapter 1:
Subsequent chapters after Chapter 2 are numbered consecutively, but they're all off by 1 (ch03.fm is Chapter 2 ... ch06.fm is Chapter 5).
If I remove the section files from the book, the chapter numbers generate correctly. If I move Section 1 before Chapter 1, the chapter numbers generate correctly. So the issue appears to have something to do with inserting Section 1 in between chapters 1 and 2.
Chapters 2 and 5 both appear after a section file. The numbering properties are set identically on all tabs in both files. Yet chapter 2 restarts chapter numbering and chapter 5 continues numbering from the chapter before it. Any idea why? I can't figure it out.
So how are you setting the chapter numbers at the book level? You can explicitly what value a chapter is to start at, especially with the intervening "Section" files. These sections should be inserted in "folders" and only then can their child files use the section numbering variable.
Chapter numbering has a higher level hierarchy than Section & Sub-section numbering in FM books. You have to plan things out accordingly for the numbering to work correctly.