Thanks for getting back in touch!
According to these forums on Flickr: https://www.flickr.com/groups/flickrideas/discuss/72157627141588468/ and https://www.flickr.com/help/forum/76980/?search=jshook, Flickr only supports transparent PNGs in the original size image. All other sizes are converted into JPG. That may be why the workaround I suggested didn’t seem to work, however you should find that the original image on Flickr has maintained its transparency.
I’ve added your suggestion for Ribbet to support saving of transparent PNGs to Flickr to our wishlist for inclusion in a future Ribbet version.
Let us know if you have any other questions or suggestions!