OK – implemented a fix that seems to be working (time will tell). Hope this helps someone else:
The issue was indeed the redirect that happens when you click the reply links. The fix was to trap the default behavior of those links (using preventDefault so that the link is not followed), so added that to the link output. In the following file on line 1612:
Was able to catch the page before the redirect (quick mouse work to hit stop before the page refreshed). The reply seemed to work correctly when I did that – the form appeared the right place, I hit stop to prevent the refresh, filled out a reply and submitted, and it worked.
So question is why is this happening with WC activated, and how do we fix?