I am having a similar issue and tried everything you list in your original post. In your last post you seem to have solved it, but what exactly does this mean?
stopping to grant PHP user access through .htaccess (by running CGI mode) and giving instead site ownership to www-data
I have this issue too. I see HTML error instead of “crunching”. The image is there, but none of the sizes are generated (i.e., there’s only the full-size image, no thumbnail, no medium, and no large).
This only started with 3.5. Was fine in 3.4.2. I tried disabling all plugins, but still happens.
I see the dropdown, but it only offers thumbnail, medium, and full size. The image is 780×780 and my large setting is 600×600 so I expect to see large in the list, but it’s not there!