I wouldn't mention it either. Some programs have GPA cutoffs, but seem to have different rules for applicants with a masters degree. This is, in fact, one of the scenarios in which I recommend a masters: it can show that you've "grown up" and can commit to being a serious student, even after a less-than-stellar undergraduate career.
Another option would be to get a letter writer to mention it, and how it's clear (to them) that your undergraduate GPA was not indicative of your potential, but your graduate GPA is.
