Try to use my mup fork: https://github.com/M4v3R/meteor-up
I also had this issue and this version works fine for me. It also updates mup to install Mongo 3.2 on the server during mup setup so you can use more Mongo features.
I had some issues with PhantomJS installation (bitbucket server returning 403) so I just disabled installing PhantomJS in mup.json.