Quote from BlueGlass:
A perfect super short charge without slowdown would actually be harder than finding xray, as a perfect super short charge (or perfect regular short charge) is 100% impossible for human beings unassisted. We simply don't have good enough timing to time our movements to 1/60 of a second.
I'm not saying I'm doing it that precise. It's just not possible. I'm trying to say that as I am pressing the run button (in an attempt to get the to breakpoint), I'm holding the button long enough to try to hit that breakpoint (which is as long as a quick tap). Also I use the environment to help figure where the breakpoint might be.
For example:
As I begin to run, I just quickly tap the run button and hope I hit the checkpoint. When I do hit the run button, let's say I pressed it on frame 20 and I happen to release it on frame 28. Then I attempt to perform that same task for the other 3 breakpoints. Of course, this means that the distance you cover is more than that of a true short charge.
However, that distance isn't short enough for the super missile. You have to stutter charge. So, I just used the key combination editor on ZSNES to do the trick.

I'm not sure how else I can explain this.