Since upgrading to WP 3.9, I cannot edit my images anymore, like editing alt text, description, alignment, links etc. When I click on the image in the editor, the previous edit button does not show up anymore.

Also the images and the text do not align anymore in the editor.

I checked various threads in the WP support forum, and the moderators seem to blame it on themes and plugins. Any idea if there is a conflict between ATA and WP 3.9 or the TinyMCE plugin (new version 4.0)? I am using ATA 3.7.12.
Did you hear anything else about this image editing issue?

I am having no problems with the editor like you mention. I would try deactivating all of your plugins to see if that fixes the issue. If it does then I would start reactivating a few at a time to narrow down the culprit.

I also had no problem after setting my sandbox site to the latest Atahualpa version (and running WP 3.9). Clicking on an image in the Visual editor caused a pencil icon to display in the upper left corner of the image, and clicking on the pencil icon brought up a separate dialog where I could enter the caption, the Alt text, the alignment, and a link for the image.