Yeah I also had poor undergrad grades 1st and 2nd year, perfect grades throughout my masters, 2 first author publications from my masters, 1 second author, plus a bunch of conference presentations. Got waitlisted last year and flat-out rejected this year in Biology (edit: committee 169, which is ecology and evolution) with a much improved application. Applying for 1st year funding for a PhD at a foreign institution. Woe is me, boo-hoo etc. I'll keep applying until I can't anymore.