I have noticed that something similar to "Importing Word documents with comments" occurs with particular users annotating the preview of documents. Their reference quotes are always lost, i.e. the quote "...this is the point on which I add an annotation..." is in the comment/annotation, but no link points me to the right page of the document preview.
Is there anything concerning their browser that could be the reason?
We have detected a bug wich can cause sometime some annotations lost, but it's not something which happen always as you describe. This bug will be fixed into "3.9.0_HOTFIX_3.0" patch, available in few days
Do you allow me to make some tests on your server to check if it's the same bug or not ?