A quantile-based confidence interval from bootstrapping can yield a 100% confidence interval that does not contain 0, i.e., with 100% of cases positive/negative. But that does not (necessarily) mean that there is a 100% chance that the new version is better than the old one. Confidence intervals are not Bayesian credible intervals and cannot be treated as such. (That said, making some certain assumptions about the underlying model can in some times allow one to treat nonparametric bootstraps in such a way.)