I think it happens with chats of all lengths for me. And clicking on the message doesn’t help. As I said, the work-around is just closing cursor and re-opening, and then I can see all the restore checkpoint buttons on all the recent messages.
I believe this is a simple UI issue (that certainly needs addressing!)
I find it will show on clicking on/off different parts of the chat - not intuitive, but it will show. It seems to require the focus to be/not be on a certain aspect of the chat.