Styles not applying to some elements, Gallery Disappears in TinyMCE, WP 3.5
Seems to be related to a chrome bug. It will be fixed in Wordpress 3.6. (see: http://core.trac.wordpress.org/ticket/24177)
It is suggested to rename the css-classes from wpGallery to wp-gallery.
Surprised to see someone with the same obscure problem as me.
What I did to work around this was move my CSS to the image's style attribute. Of course I had complete control over the elements being rendered... not sure if it'll help in your case.
Looks like a simple workaround is to go through the tinymce.activeEditor.contentDocument.getElementsByTagName('img') elements and set element.className = element.className. (This can be added in many handlers like onClick, onChange, etc. to prevent the weird state when the class doesn't apply itself.)
This seems to be a good workaround, but I would like to know how/why TinyMCE with Webkit gets in this odd state though.