Rotating image does not work for custom image sizes

From examination, it looks like a bug. I can’t think of a good reason it shouldn’t apply those changes.

Reported: http://core.trac.wordpress.org/ticket/19889

Patch in that ticket fixes the problem.

Also, in response to your other question, you can define IMAGE_EDIT_OVERWRITE to true in the wp-config file to make it not create those oddly named files and to just overwrite the original names. This will break the “restore image” capability of the built in editor though.

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