So , I'm using the same version 2.5 on Mac. Normally I just drag my files down into the window of the encode tab. It doesn't ask me anything about the photo file. Instead of dragging into the window if I click add it lets me direct it to a folder but no mention of the jpeg in the file. Sad thing is I feel like I've done this before and I just can't remember the trick.
Edit: Figured it out. Go to the tags tab. From there it will ask if you want use the photo in the file when you hit write tags. After that encode....Eureka