I work with Bento and am now looking into this (sorry for the delay, but we've been on holidays over the New Year).
Anyhow the problems persist. To help solve them, i've double checked your
- Did this happens only with one special image or with all images?
- Did you try with an image fresh uploaded? Did you try the dummyimage yourself?
Happens with all images as well as a freshly uploaded dummy image.
With a freshly uploaded image, I do notice something, however. When I click on "edit image" I can see it has these dimensions: 2448 × 3264.
But when I click into Crop Thumbnail, it comes up with a "raw" size of 0x0. That appears to be the heart of the problem. Crop Thumbnails is not picking up the raw dimensions and thinks no size exists. See this screenshot.
One difference with our set up (which is still in development), is that our images aren't stored in the same location as our WP install. Because of remote developers, we're storing images on Amazon...