This is the bit that troubles me. In fact, a similar phenomenon nearly cost me a job while I was in grad school. I applied for a position with the CS department, and my future boss had received some emails from a guy with the same first and last name, but different middle initial that were, let's just say, quite unprofessional. It's only because I was told and given the chance to point it out that I got the job.
I could probably have lived without the job in this case (it was only a 20-hour a week student job, after all), but what if it weren't? My name is common enough that unless you know something about me beyond first and last name, you won't find me on the internet. I'm practically John Smith (not my real name, obviously).