If Thunderbird opens in the last message of the Inbox
No matter how you sort your messages in the Inbox folder, you may face this strange situation, when Thunderbird opens always selecting the last (bottom) message of the Inbox, or always the first (top) one. If you have this problem, don’t bother playing with Thunderbird’s native options. Most probably you use an add-on that is responsible.
Open Thunderbird Add-ons and check if there is in the list the “Select Inbox” add-on. “Select Inbox” automatically opens the Inbox folder at the startup of Thunderbird, even if in the Thunderbird options you have selected the opening of a Start Page.
To change how exactly Inbox will be opened, press the “Options” button of this add-on, and see what “Message Selection” suits you best. If you choose to avoid completely message selection, then Thunderbird will open in the Inbox folder without any message being selected (message preview will be blank).