Well it appears I am not the only person having a problem with thunderbirds marking emails as read.
This is how I use thunderbird
I have disabled the “Automatically mark message as read” functionality so that I have to set messages as read. If I don’t do this many emails were being marked as read when I hadn’t really finished reading them or replied to them.
In my case I classify an email as read when I have replied to it or clicked the read button (they require no reply)
I just want Thunderbird to set the read flag when I reply to the email.
Also I normally view the email in the “Message pane (F8)”
I get exactly what I want. Thunderbird now sets emails as read, when I reply to the email.