I myself abandoned bootbox.js for the same reasons. Not only is it a little wonky on different devices it also requires jquery. I just went with ionic's own http://ionicframework.com/docs/api/service/$ionicPopup.
It looks like you're missing dependencies when on device. If the popup behavior isn't happening its the .js if the popup behavior is happening but no styling then its probably bootstrap.css that's not being loaded.
Check the network panel when inspecting to see the issue.