I had this issue as well. A fix that worked for me was to update my DC to latest version. Then open the PDF and go to Tools -> Comment to show all the text boxes in the right sidebar. Then highlight all the comments in the right sidebar (hold Shift, click the first box, then scroll down and click the last box). Then right click one of the boxes -> Properties. Slide the Opacity slider all the way to 0, let the screen render, then slide it back up to 100%. Then save the PDF. The boxes all readjusted. ¯\_(ツ)_/¯
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