well, i guess you can't do much about it. if it does'nt show up in any other view, it probably won't effect you very much, so all i have to suggest is to forget about it and continue with your logo. when it is finished, please post it i would like to see it!
It WILL make a difference because I hope to take screen shots, crop them out, and use them as frames for an animated GIF, meaning any imperfections in the Perspective view port will show up in the finished project.
As for what logo I am trying to make, I am trying to make the logo for this series of YouTube videos called WTF Pokémon. The first episode is here:
http://youtube.com/watch?v=zhFsIkzs-jo (http://youtube.com/watch?v=zhFsIkzs-jo)
The series is from the Smash Boards (the world's largest and most well known forums for the Super Smash Bros. series of Nintendo video games) into a 3D spinning logo.
Also, I have it saved from before the problem arized, BUT THERE IS NO WAY TO GET RID OF IT!
Sorry for the caps lock, but I'm in a bit of a panic right now. I saved it once then came back to it and was greeted by this problem.