That is unfortunate. It is particularly problematic because if you update the cross-ref a second time the added rows disappear completely.

I don't pretend to know why this might happen but the behaviour of inserting content at the same point as the start of a bookmark is the cause. A couple of workaround suggestions to avoid this issue are:
1. Put your table captions above the table. IMO, table captions below tables doesn't work well with how people use a caption. If the table breaks across a page, having the caption appear after the first page of the table is not very user friendly.
2. Include an empty paragraph between the table and the caption. If you add this empty paragraph in front of the caption, make sure the cross-ref doesn't include it when it updates. You can also make this empty paragraph hidden (in the font dialog) to hide the fact that it is there.

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Andrew Lockton
Chrysalis Design, Melbourne Australia