Our solution to that is to always rebase & push right before you run through ci & merge. As well as updating the PR diff to be against the master it was actually merged against, this also has the advantage of making your git history a lot more linear[0], which has various other upsides (e.g. makes it a lot more sane when using fugitive or something to navigate backwards & forwards through the history of a file).

[0] i.e. looks like http://blog.carbonfive.com/wp-content/uploads/2010/12/multip...