I’m hoping @Elena Stofle and @Thad Woodman will have a look at this :)

This is actually a really problem -- I have a couple excerpts in this situation, and I’ve had people tell me they have stopped providing feedback in frustration, as they can’t  see their comments after posting them. It is a problem for the author too, as the email notification sent out when a comment is added doesn’t provide the context for the comment (doesn’t show what they were commenting on) -- the only way to see that is to follow the link to the excerpt, but then that doesn’t work because the comment is hidden under the pile.

One possible solution to this is something which I believe could be implemented relatively painlessly through some updates to the Javascript and CSS (for those not in IT just ignore the technobabble)...

Currently, all comments are displayed in full, and take up a lot of spaces, which is part of the reason for this problem. Instead, I would suggest when the pages loads comments are displayed as only an icon / bubble in the margin, identifying the author (and maybe the date of the comment. Hovering the mouse over the icon could display the comment in the tool-tip, and clicking on it could toggle the comment into full display, including the ability to reply to the comment etc. This would enable many comments to stack in the margin and still be accessible.

Other user interactions which would make this experience nicer would be: hovering over highlighted text could emphasize the comments linked to it (e.g. change their border colour). Hovering over comment bubbles could highlight the text commented on (e.g. change the highlight colour).