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Description
Since Domon is a little woozy from the heat in that last panel, I'm going to go ahead and just transcribe that first bit of his text for everyone: "Whew, I forgot how much fire we used to make that molten glass... Anyways, that's everything I know about this problem. I'm afraid I can't give you any further insight."
A full transcript of the entire text is available upon request, as always.

About the "Physics" button:
When you open MMD, this button is ON by default. What it does is toggle whether or not a bone will fall under the control of the physics engine when you register a keyframe. (This is assuming that the bone in question does not have static physics that always ignore the physics engine.) This is the reason why a model's hair, skirt, or boobs register their keyframes with an "X" symbol instead of a diamond. The "X" means that the physics engine has control (if turned on) while a diamond means it does not and you can manually manipulate the bone.

ANYWAYS yes, this is not a true answer to the cause of the problem, but this issue has been floating around for quite a while now , and all other tutorials and links to solutions are DEAD! So I decided to go ahead and share what I know. While writing this, it also came to my attention that External Parent settings may also be a factor in this glitch.
Whatever the cause is, the end result is that your model's dynamic rigid bodies (the ones controlled by the physics engine) get YEETED off to Narnia, and everything that follows them (bones, joints, pieces of the model itself) gets dragged along for the ride.
I ran into this issue when making my Sand Planet video (which, incidentally, had some crazy external parenting setups going on) and eventually I managed to translate a fix buried several pages deep on a Japanese MMD forum. I'm not fluent enough to reach out and ask for more information, but the fix worked for the people on the forum, and it also worked for me. So I'm sharing it with you guys now.

Model Credits:
Miku model by 大葉真琴 (from bowlroll)
Domon Kasshu canon outfit model credits in the description here
Sand Planet PMM file credits in the description here (because I'm lazy and don't feel like retyping everything over 9000 times)
Interactive Touchscreen and screenshots made by me

MME used:
HAToon2改変_アニメトゥーン
Iridescent
Post Alpha Eye
HG Point Light
g_ALB_01
Working Floor

Description
Since Domon is a little woozy from the heat in that last panel, I'm going to go ahead and just transcribe that first bit of his text for everyone: "Whew, I forgot how much fire we used to make that molten glass... Anyways, that's everything I know about this problem. I'm afraid I can't give you any further insight."
A full transcript of the entire text is available upon request, as always.

About the "Physics" button:
When you open MMD, this button is ON by default. What it does is toggle whether or not a bone will fall under the control of the physics engine when you register a keyframe. (This is assuming that the bone in question does not have static physics that always ignore the physics engine.) This is the reason why a model's hair, skirt, or boobs register their keyframes with an "X" symbol instead of a diamond. The "X" means that the physics engine has control (if turned on) while a diamond means it does not and you can manually manipulate the bone.

ANYWAYS yes, this is not a true answer to the cause of the problem, but this issue has been floating around for quite a while now , and all other tutorials and links to solutions are DEAD! So I decided to go ahead and share what I know. While writing this, it also came to my attention that External Parent settings may also be a factor in this glitch.
Whatever the cause is, the end result is that your model's dynamic rigid bodies (the ones controlled by the physics engine) get YEETED off to Narnia, and everything that follows them (bones, joints, pieces of the model itself) gets dragged along for the ride.
I ran into this issue when making my Sand Planet video (which, incidentally, had some crazy external parenting setups going on) and eventually I managed to translate a fix buried several pages deep on a Japanese MMD forum. I'm not fluent enough to reach out and ask for more information, but the fix worked for the people on the forum, and it also worked for me. So I'm sharing it with you guys now.

Model Credits:
Miku model by 大葉真琴 (from bowlroll)
Domon Kasshu canon outfit model credits in the description here
Sand Planet PMM file credits in the description here (because I'm lazy and don't feel like retyping everything over 9000 times)
Interactive Touchscreen and screenshots made by me

MME used:
HAToon2改変_アニメトゥーン
Iridescent
Post Alpha Eye
HG Point Light
g_ALB_01
Working Floor