As you may know, in the PAL version of Star Fox 64, the game stops counting your points when you get 511 points in a single mission. (This is by far easiest to do in Area 6, but it can also be achieved on Meteo with a great amount of effort) But, in the NTSC version, you can get more than 511 points; in fact, on NTSC 999 is the maximum allowable score for one mission. When you have a score of 512 or higher in a single mission in the NTSC version (we'll say it was on Area 6) the game treats your score normal at first. But, when you complete the game and enter your initials to add your new total score to your Rankings, a strange glitch will occur.
The game will subtract 256 points from your Area 6 score, and also your total game score.
However... the score is still ranked as its actual value. So if you score 2256 Total Hits as well as 512 or better on Area 6, your total will show as 2000 but will be ranked like it was 2256. (If you are so good that you can get 512 or higher on Meteo, and then you go to Area 6 and get at least 512 points there, then when you finish the game and enter your initials, the game will subtract 256 from both your Area 6 AND Meteo scores as well as 512 from your Total!)
Another oddity is that if your Area 6 score is between 512 and 555, it will look like you didn't get the 300 points needed for a medal, but you'll still have the medal symbol next to your score! Cool!
The big problem with this glitch is that it prevents you from ever seeing your real score again after you have entered your initials. As a result, if you want to send me a picture of your best Total Hits score for the NTSC version, I would strongly suggest that you take the picture at the congratulations screen where you enter your initials, because you can see your real score here. (If you don't have a camera handy at the time, you can stick a tape in the VCR and record it, then photograph it later.)
If you do this glitch repeatedly, your Rankings will become messed up even more. If complete the game again and beat your new glitched score (or actually, the score as it appears in the Rankings, in the above example it would be 2000), and you get 512 or more hits on Area 6 this time too, the score will be ranked above your previous score after you confirm your initials, but then 256 points will be immediately subtracted from it. So if you scored 2056 points this time, it'll show as 1800, but it will appear above the score of 2000! If you continue to do this, your top ten scores will become completely out of order!
A nice side effect to this bug is that if you always use the route to get high Total Hits scores (CO-ME-KA-SX-MA-A6-VE) and you keep getting 512+ on Area 6 or Meteo to screw up the Rankings, you can take other routes through the game that you can't score as high on, and you can still make your top ten! I placed second in my top ten Rankings by taking the very bottom route (CO-ME-FO-SX-TI-BO-VE) with a score in the 1700s, despite the fact that I've scored well over 2000 points numerous times on the other route. You can use this to your advantage to make pictures of your best scores on missions that are not on the CO-ME-KA-SX-MA-A6-VE route if you did not have a VCR or a camera avaiable at the time.
For a more technical description of this glitch, please read this page (written by Steven Brown).