I'm having the same problem that was described in this post http://wordpress.org/support/topic/enable-media-replace-not-replacing-anything-but-full-sized-image?replies=4 and I was wondering if anyone knew if it was fixed, or if there was some kind of conflict with the new WordPress version and I just need to be patient.
Like the poster of the above topic, I made a test page with a full-size, large, medium and thumbnail version of the same image (was called IMG_0868.JPG and is an image of a woman and a dog in a canoe) and then I replaced it (updating links) to a new image (IMG_0808.JPG which is a picture of a dog up close). The full-size image updated and the other sizes are just links that say "IMG_0868.JPG" even though when you click on them, they show you IMG_0808.JPG, the new image.
When I looked at the text version of the page, the links were all changed, but the source and alt tag were still listed as the original image.
The link to my test page is http://www.maddielabstudio.com/test-page/.
I hope this problem gets fixed soon because this is usually such a useful plug-in and usually saves me so much time.