Aquamail groups conversations based on one of the two factors:
1. Headers that are generated by the e-mail app/program used to do a response/forward, etc.
(In-reply-to: and References: that have common message-id numbers)
And in this case, "break on subject change" will break the conversation or not when the subject is different (excluding prefixes and suffixes such as "Re:" "Fwd:", etc.)
2. (if configured) by the combination of the sender/recipient+subject.
First of all, the subject of the autoresponse is completely different. So, even if there were headers that were linking the messages, "Break on subject" would separate that autoresponse from the conversation thread.
But in this case, the autoresponse is most likely generated by the program that does not do a thorough "reply", but just sends a message to the address, and so, it doesn't include any reference to the original message in the headers. (I see that you just posted response that changing "Break on subject" didn't make any difference.)
Finally, even if you enabled the option to use the scenario 2 above, - the subject is different, so, Aquamail wouldn't combine them using that scenario.
This addresses the issue of the "autoresponse" message.
I don't know why the response from your correspondent is not grouped in the Smart Folder. It might be related to the settings of which messages should be included in the Smart Folder (only unread, etc.) Sorry, I am not using Smart Folder myself, so, I have limited experience with that. Somebody will respond to you about that...
