"All sizes except thumbnail" save does not work

[worldwisewebs]

To reproduce:

1. upload a new image, click the edit label
2. click edit image button
3. perform a crop on the image
4. Under "Thumbnail settings", "Apply changes to" select "All sizes except thumbnail"
5. Click save button underneath image crop

Bugs:

• thumbnail will have proportions of the crop made, despite the setting
• click edit image again, the Thumbnail Settings box is now gone.
• Clicking restore original image restores image but thumbnail settings box remains missing

Screenshot of edit page without thumbnail settings box: ​http://www.diigo.com/item/image/23e4l/vud8

I had this until I realised that 'Crop thumbnail to exact dimensions (normally thumbnails are proportional)' was not checked in media settings screen.

This seems as a server issue. Can you put here the server configuration or the host you are using.

This happens regardless of the "crop thumbnail to exact dimensions" setting. I had it on, but have confirmed with it off as well. I've tried this on two servers now, one with a local provider that we use:

​http://sandbox.fromhere.org/phpinfo.php
Linux vhosts2.main.nc.us 2.6.32-5-686-bigmem
PHP Version 5.3.3-7+squeeze14
MySQL 5.1.66

Also on bluehost:
​http://worldwisewebs.com/phpinfo.php
Linux box545.bluehost.com 2.6.32-20120131.55.1.bh6.x86_64
PHP Version 5.2.17
MySQL 5.5.28

Same results on both sites. Both sites are testing with no plugins active and the 2012 theme active. These are both test sites so I can provide logins if needed.

Confirmed this and it's a bug caused in 3.5

After playing it's the same issue as #22985. Closing this one since that ticket shows what the issue is.