TOC scrambled with headings from anchored objects

I have a book design with first-level headings in the main text flow and second-level headings inside of anchored objects in the left margin of the pages. When I generate a TOC the headings used to be in the correct order, precisely as intended. After installing the 5.0.2 update however the TOC gets scrambled when I update it. The second-level headings from the anchored objects are printed before the first-level heading (in the TOC) when they are both on the same page. Second-level headings on pages after the first-level heading are printed after the first-level heading (in the TOC) where they should be.
The source of this problem may be the altered search-order for headings that should be included in the TOC. Although it seems only logical that the main text flow defines the order from top to bottom and anchored objects should be included from the anchor in the main text flow. Now it seems that the search order is from left to right on the pages.
Adobe says to have made major fixes in the areas of both anchored objects and table of content generation, but whatever they did the only difference I find is for the worse.
Is there a fix for this fix?

Long shot, but go to the application preferences and uncheck the box in the General section that says Prevent Selection of Locked Objects.

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