We had a lot of trouble with the publisher tools too. More broadly we want to try and automate the package process so every commit is packaged up. So, rather than trying to get the publisher tools to work, we instead decided to make a Node.js package which handles the upload for us. It worked too! Once the package is done going through the review phase, the package will be back up on the store, this time right up to date.
All the best everybody and keep up the awesome!