Not having this issue either. Don't worry though, I really really doubt that it's more than a software issue. Only thing is I don't know how you'd go about fixing this. Maybe call Apple and ask them how to reinstall the files pertaining to Retina Spotlight search?
Must have been a small software glitch. It's weird though. I assumed it was because you restored from a Time Machine backup of a non-Retina Mac and some of the non-Retina elements overwrote the Retina ones. But that isn't the case.
Glad it all worked out, though. Enjoy the MacBook!