Do you have a sample doc you can post here for someone to test?

It is possible that the Heading level and the outline level is not exactly matched but it is also possible that there is some piece of hidden content sitting in front of the headings that is interpreted by the pdf engine as raising the outline level for the following item.

You could try removing the content preceding the problem headings and sending to PDF to see if that resolved the level issue. If you can identify the exact point causing the problem then you could replace it with unformatted text to 'remove the corruption'

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Andrew Lockton
Chrysalis Design, Melbourne Australia