A very bizarre problem with InDesign

Can you show a screen shot of how your text frames are laid out? Are they individual frames, or threaded?

e.g. ID normally reads text frames from left-to-right and top down, which can get confusing if there are a bunch of separate text frames. Even if they are threaded frames, it will list in order within that thread no matter where the separate frames show up. So in my example here, the top two poems are a single threaded  story starting with Alpha, but I've moved the second part of the thread up to the left, but the text frame in which it starts is still actually to the right of the one containing Chi. So, ID reads Chi first, then the text frame with Alpha (and consequently Beta) next, then ends with Delta.

Just about the only reason this would happen is if the poems (or titles) are in individual text frames, and the frames were drawn in reverse order and then copied across all the content pages.

TOCs work best with single flows of text, or a few organized text flows. If you start running text through individual text frames, it's easy for them to get out of order (a nearly invisible thing in layout), and so it picks up the content in wrong order. (That is, the frame on the bottom is visually and logically the second one, but if it's the first in page structure, it will be treated that way by processes such as TOCs.)

The only easy solution would be to re-flow all of the content into properly structured pages, which ideally should have NO text frames on them except the single primary frame deriving from the Parent page(s). Any spacing or separation should be done entirely with paragraph styles, not by breaking text into separate frames on each page.

I can't think of any second reason this would be happening.