I just happened across this old topic and thought I'd comment since I did exactly as the original poster stated. My last two years of undergraduate were not good, and so I did a master's degree to try and overcome that. Even though I got all A's and A+'s in my master's degree classes, I don't think graduate schools overlooked my undergraduate record. I have a good amount of research experience (3 academic papers and 5 years of industry research) and a strong PGRE for a domestic (890), however, I still only got into 3 of the 16 schools that I applied to (UMD, JHU, and Davis). Judging by other profiles, I feel that if I instead got all A's in my undergraduate classes and foregone the master's degree, I would of gotten into more of the places that I applied to. Don't get me wrong, I'm quite happy with my choices. I'm sure my master's degree helped, but it didn't fully overcome anything.