Same problems here with two sites.
The first site was a timthumb issue in most cases, but there were some files in both the uploads folder and themes area it skipped with no pattern.
On the second site most of the files it skipped were in the uploads folder so I installed the ‘Replace Image’ plugin and used the PageSpeed extension for Chrome to get the compressed versions of the images to replace manually one-by-one.
For the files NOT in the uploads area I am stuck because I don’t have FTP/Shell access so I cannot touch those.
Example path of files that won’t compress and I cannot reach them:
https://site.com/wp-content/themes/innerhop/img/tip_border_grey_up.png
The rest were in the uploads so I could manually fix em..
I would be happy to PM a URL but I don’t post real site URLs online.
EDIT: Here’s the details from the media section:
Optimize Media Library
…
30 images in the Media Library have been selected (0 unoptimized), with 335 resizes (0 unoptimized).
Optimize Everything Else
…
Last optimization was completed on September 30, 2014 at 1:18 pm and optimized 324 images
…
There are 686 images that have been optimized so far.
(So no, I didn’t skip the ‘Optimize Everything Else’ choice and ‘Remove metadata’ was NOT enabled on either site.)