Tom,
I disagree with this statement in relation to my comment about BIAB not being like sheet music.
That's bad enough, but they don't say so. In fact, they have gone to great lengths to conceal it.
Since I started using BIAB in 2006, I've only ever known it to be performance software. As far as I'm aware, it's never pretended to be anything else.
Is the below what you are after?

The bars for each section are correct given what I've enetered. Two times through the first section (16 bars) means the second section starts on bar 37. Then two times through the second section (12 bars) means the end will come at bar 61 (as shown).
If so,
here's a link to the SGU file.
I wonder if you have been entering "1" in the repeats instead of "2" ?
It sounds like you might be thinking "once through and then one repeat" and so you put "1" in the number of repeats. BIAB, on the other hand, is interpreting the number of repeats as the "number of times through a section" so, if you want a section to play twice, "2" needs entering.
For the record, I'm a user like you. I am not a representative of PG Music. I spent time putting this post and my previous posts together for you because I could hear your frustration.
If I get a chance tonight, when I come in from work, I'll detail how I entered the repeats.
Regards,
Noel