Something seems to be happening to the leaderboards--a bunch of the (legitimate) top players (including Kyoshi Yozima) just got deleted (along with the hackers). I got deleted twice in a row, but got myself back on both times by improving my time on a level.
I've also been experimenting with the warp zone times on XBLA and Steam. The key difference between the two versions seems to be that the warp zone completion bonus is subtracted from your global time immediately on Steam, but waits for you to improve a level on XBLA. On both versions the bonuses are taken away once you improve a level time after
restarting the game.
On the Steam version, each non-character warp zone gives you a 15 second bonus. I was also able to lower my time (~7 seconds total) by speed-running the Commander Video and Flywrench levels (I saw my global time fall on each improved attempt). Jill, Ogmo, and the Kid's warp zones didn't go down when I attempted to speed-run them (but I could just be too slow).
The total bonus time I was able to achieve was 231 seconds (15 * 15 + 7)--which corresponds nicely with my previous attempt to lower my time on XBLA.
For now anyway, it seems the best plan--for anyone who really needs
to keep their times low--is to redo all of the non-character warp zones before working on your speed runs--every time you start the game.
Of course, all of this presumes that we can manage to keep ourselves on the leaderboards at all
And now I'm deleted again
--everyone over 307 is now gone.