Dear pseudononymous,

It is a positive you finished strong. When combined with your performance in your master's program, it should alleviate any concern about your ability to succeed in the classroom. Schools only report the undergraduate GPA in the GPA measure, but look at your entire performance in all degree programs when evaluating your candidacy. Bottom line: don't worry so much about your GPA being a negative. I do think, however, you should probably acknowledge in your application that you realize the first two years are not pretty and that your last two years and master's program are the true indicator of your ability.

Good luck,
Lisa