This question may be related to a resolved thread.
Since updating to EE 2.3.1, none of the updated sites are able to save resized images to disk. This includes thumbnails as well as custom sizes. I have not found any changes I can make to the file system that makes any difference.
I wish I had reported this when I first discovered it because now my memory is a little hazy. I *think* that it worked correctly in 2.3.0 but something changed in 2.3.1. It definitely worked correctly when the auto-resize capability was first introduced then stopped working after an EE update.