Well its been awhile, I've been looking over the code recently and fixed a few issues that were stacking up. You can grab the latest version [here].
-Fixing it so images won't always save with an alpha channel, even if alpha is disabled.
-Adding File Association support, so users can now set up BrushTone with "Open" and "Open With" to quickly load an instance of Brushtone with the selected supported image. Note that each time an image is loaded this way it will open a new instance of BrushTone, to load images in an existing instance you need to use the load option in the Canvas Menu. File loading unfortunately is still limited to the directory BrushTone is in but this can help side step that a little.
-Removed the JPeg and BMP options when saving images. As it turns out Pyglet can only save PNG images, so whatever files may have been called with previous versions, they're all actually PNGs. Not too happy about that one.