Very common question. Here's some background info on what you're seeing and how to address it.
First, the "Order" panel is mis-named.
Given that there are 4 reading orders in a PDF, calling one panel "THE" ORDER panel is pure nonsense because it shows only one of the four ROs. The 4 ROs in a PDF are:
- The TAG RO (aka, the tag tree)
- The ARCHITECTURAL / CONSTRUCTION RO (aka, the "Order" panel)
- The TAB RO (keyboard access)
- The FORM RO (for <Form> fields)
And they have little (if anything) to do with each other!
Only the TAG RO is required to meet the PDF/UA-1 standard requirement for accessibility. Many in the industry ask why even care about the Architectural/Construction RO, since it's not required. Here's why:
- Many technologies used by those with disabilities do not use the TAG RO, and instead use the Architectural RO. Technically, they do not conform to the PDF/UA standard, but our end users don't usually give a rat's patootie about that and just want something that is cheap (or free), easy to use, and helps them read the PDF.
- No one has the right to tell a user which technology to use, such as requiring them to use a higher-priced PDF/UA-compliant screen reader.
- Other technologies, other than assitive AT technologies, use the Architectural RO as well.
- You want to reach the widest audience possible, regardless of what technology they use.
So yes, the Architectural RO shown in the "Order" panel is based on the exact sequence of how you created the different frames/elements in your layout. And that mostly does not represent what you want in the TAG RO.
In InDesign, you must learn how to control both ROs:
- Control the TAG RO with threaded stories (frame to frame) and the Articles panel (optional).
- Control the Architectural RO through the stacking order in the Layers panel.
In my classes and books, I teach several ways to do this.
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