(Running 3.99.0git95) Folder with unread messages. Configuration>Preferences>Fonts (Fonts may be changed; but this is NOT required) Each click on Apply marks next unread message read.
What happens is that the current folder/message list is reloaded when applying fonts, so depending on your "Open message when selected" settings, this can cause a message to be opened. Clearly, when the the folder list is reloaded for this reason, the "Open message when selected" options should be ignored and the current state should remain.
Also: - Mail Handling>{Receiving, Sending, Proxy} - Message View>{Text Options, Image Viewer, External Programs} - Display>{Colors, Summaries, Themes}