Puzzle: Multiple text threads causing content of others to shift, except the first spread

Found something interesting & I'm not quite sure what's causing it - 

Basically, I have some pages with two unconnected threaded text boxes.
When I fill one up the text flows normally.

However, when I fill the other up after the first (in this case, big frames first, then small upper frames), all the content of the bigger frames gets pushed and doesn't start again until the content of the other frames ends.

Adding text in the small upper frames seems to add pages that won't connect properly. In this shot, you can see the thread from the last "big box" going straight down, where it connects again many pages later. 
Strangely, the content on the first page is fine. (Well, maybe it's not strange, but I don't remember seeing this before... 🙂 ) And the file gets weirder every time I change stuff.

Any ideas what's going on here?

I have some experimenting to do...

thanks!