Changing the EXIF data is exactly the wrong way to do it. This is only supported by some programs, so when you for instance upload your picture to the net, it will probably be the wrong way around if you rely on the EXIF data. Xee rotates the image data itself losslessly.

I might re-enable the automatic saving that 1.0 used as an option, but it's been disabled for now because most people don't expect a "rotate" feature to immediately change the data on disk.

Apparently there is some kind of bug where cmd+s doesn't work. I've never seen this happen myself, so I'll need more information about this before I can do anything about it.