I had applied for a position in a very large company and did not get it. Years latter I was hired by the same company, but in a different branch. I once mentioned to my boss that I had an interview with the company years ago (but as he knows I hadn't worked for them before). Was this a bad thing to reveal? Does it depend on the boss? I know mine has a philosophy of "avoiding turning heads" and may see it as a negative thing that he hired someone that another colleague didn't.
You are not a "turning head", you have never worked for this company. They just couldn't hire you at the first time. Which doesn't necessarily mean they didn't like you. Even if so, you may got better. Time passes, people change.
I know a lot of people trying to get work in big companies and they had more than 2 interviews at different times. Lot of them finally got there.
I have personal experience when the interviewer from the company where i failed to get a job, 2 years later asked me to come again for the interview for the same position.
So, I don't think your first interview should make any sense here.
I can't imagine how this could affect your boss's perception of you in a negative way. He obviously thought enough of you to hire you in your current role, and your performance should certainly be a more important aspect of his perception than anything that happened previously. That's especially true if your previous attempt at landing a job with the company happened years ago.
Being turned down for a particular position does not necessarily mean that you have any personal or professional deficiencies. Maybe the previous hiring manager found a better fit based upon specific skills, internal considerations, or team personality. A perceptive manager would realize this and would not hold your previous experience against you.