As per the linked gif, at times when selecting orders and backing out from the order selection screen, they don't appear in the list regardless of having the 1/2/3 confirmation numbers. The orders will NOT receive progress in the event of this happening.
It requires a bit of jiggling around to get them to work properly.
http://i.imgur.com/WVY6UiH.gifv
That definitely seems to be a bug. I'd recommend you report it to our support team so they can document the issue.