Go to mail with one mail folder open Double click on some other folder in the list of folders New folder opens correctly Go back to old folder. Note that it's contents are the contents of the new folder
Use right-click on the second folder and select Open in New Mail Window. Otherwise, a duplicate of bug 67271
Stephen do you still encounter the issue (if so look into your preferences to make sure to open mails in new windows.)? Setting up close me in 3 weeks.