Thank you for your post. When creating comments/notes in Adobe, you must make sure that you are flattening the map when saving/exporting. Avenza Maps does not support multiple layers on import, so it is likely that the comment layer is getting left out when processing. You should see the options to flatten/optimize PDFs in Adobe under either the File > Print or File > Save as > Optimized PDF settings, depending on what version of Adobe Acrobat you are using.
If you are still having issues, please don’t hesitate to reach out to our support team via help.avenzamaps.com and we would be happy to help further!