Preview bug regarding Table of Contents and Annotations

I'm involved in a paperless pilot project and am having a difficult time circumventing an issue in Preview.
I'm re-formatting material for executive meetings from WordPerfect, Word, Excel and PowerPoint into bookmarked PDF format in Adobe Acrobat Pro X. When they are opened in Preview by senior management on MacBook Airs, the Table of Contents links everywhere correctly. However, the moment they add an annotation (in this case, notes), the table of contents is thrown one page off, regardless of their place in the document. Even after removing the note, the table of contents does not revert to the proper place. I'm assuming this occurs because the annotation throws off the markers from the imported bookmarks.
Using Acrobat Reader on the Airs isn't an option since annotations aren't possible. We are also really trying to keep production of the PDFs limited to Acrobat Pro to ensure cross-platform compatibility of the Table of Contents.
Has anyone else encountered these issues? Is there a potential workaround?

A lightweight alternative to Acrobat Pro for creating a TOC is PDFOutliner ($5 on the Mac App Store.) Adding annotations later to the PDF does not affect the TOC generated by PDFOutliner.
Note: I am the developer of PDFOutliner.

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