The culprit is the flattening process.
With flattening, any form field information gets lost, while the field value becomes part of the base PDF, and it does not have any structure information, making it very difficult for the screen reader to find the data from the flattened field (it is probably at the very end of the page).
One possibility would be to recreate the PDF instead of flattening it. (well, is there a need to flatten; would making the fields read-only be sufficient?)
Hope this can help.
Max Wyss.