How to fix physics simulation in MMD

First, you should enable Trace Mode from physical operation. Trace Mode allows you to calculate & stop physics while editing motion.

Then, move to starting position and register skirt keyframes.

Click on Null_149 (you should find スカート in Japanese mode) to select all skirt bones, disable physics from bone manipulation then click register. Now the registered keyframes will be diamonds rather than crosses.

After that, move 1 frame and do the opposite (enable physics and register). Keyframes will look like this:

This isn’t perfect but makes it a little bit better.

credit: 驪駒早鬼 by 塩蛙