I used Thunderbird 31.1.2 which is an excellent email threader.

Well turns out that stash notifications dont thread in Thunderbird which means they must not be setting mail headers that indicate how to thread

Namely References: and In-Reply-To:

I see the MessageID is being set

<JIRA-servicedesk-1251-3633907232089080@Stash>

But the IN-Reply-To is not a reference to a message id but some generated thingy

<JIRA-servicedesk-1251@Stash>

If it used the originating MessageID it would thread!

See - https://wiki.mozilla.org/MailNews:Message_Threading