Does anyone know why there would be a difference/what the difference is between the "tracked opens" that you see on an individual mailing report and the "confirmed opens" you see when you run a mailing report through the reports section of CiviCRM?
The Mail Summary Report shows each time the mailing is opened, rather than the number of contacts who have been tracked as opening it (whether once or ten times). Current versions of CiviCRM show the "tracked opens" by counting each recipient no more than once.
Just to throw a wrench into the works, many opens aren't tracked at all. CiviMail (and all mailers that track opens) uses a transparent one-pixel image with a unique URL for each recipient. When someone opens the email, the image gets loaded, and CiviCRM knows the recipient by the URL.
Now, many email clients don't load some or all images by default. If the image isn't loaded, CiviMail can't tell the email has been opened. This can skew open rates low.
It's still a valuable measure, especially in comparison message-to-message, since presumably you'll have the same mix of image blocking among your recipients. However, know that the number won't include at least a certain portion of people opening your message.