If I understand this correctly, you have a page that looks like this:
11111111111111111111111111111111
11111111111111111111111111111111
22222222 3333333333 444444444444
22222222 3333333333 444444444444
55555555555555555555555555555555
55555555555555555555555555555555
and you want the order to be as indicated by the numbers. If that is correct, I see the problem. You are running into a limitation of touch-up-reading-order's ability to display the order. If things are in the right order, it displays as one big block because all of the elements ARE in the correct top-to-bottom and left to right order.
In order to see whether they are in the correct order and to see the effect of trying to change the order, you can use the Tags panel which is a more advanced (and harder to use and understand) interface. Here is what to do:
1. open the tags panel (view >nav panels > Tags)
2. In the tags panel, there is a popup menu labelled Options or with a gear icon. Click that and select Highlight Content.
3. Switch to the text select tool and select some of the text in the "11111" paragraph. In the tag panel, click the gear/option menu and select Find Tag From Selection. This should show you where in the document's structure that first paragraph is.
4. Now, you can click in the tags panel on following paragraphs and a box will be drawn around the content.
If your columns are in the correct order, you should be able to see the rectangle around them as you click on successive paragraphs in the Tags panel. You can use the Tags panel at the same time as touch-up-reading order to see the effect of selecting a region and clicking Text (or another tag).
After you get the hang of it, it isn't too much harder than the basic reading order panel.