These are 3do problems. I suggest reverting it back to the one with the legs that are "in the ground." Does the fist and weapon look correct on that one?
The problem with JOKE is that it messes up the 3do file. A text editor is necessary when 3do editing:
Players and enemies have a 3do offset, which basically makes the 3do work in an offset position in game.
Open your 3do with a text editor.
Put this in for the offset:
"INSERT OFFSET -0.000050 0.000000 0.120114"
If you have a zero offset then the players hip will be level with the floor, and his legs will be "in the ground"
Here is a fix for if your 3do looks scrambled in the game:
If you are using a kyle katarn - style model, using ky.pup:
Have ky.3do ready.
Import your one into JED via "import 3do"
Now go to tools -> 3do hierarchy -> load load the ky.3do hierarchy.
Now export to 3do, and manually add the offset that I said above.
The 3do hierarchy is basically how the 3do is built, and what child/parent objects are. Like thigh -> calf -> foot. JOKE has been known to mess this up. It is found at the bottom of the 3do file, but I don't suggest editing that directly as you don't know what you're doing with it.
But from what you said it just seems like you just need an offset!
This is retarded, and I mean drooling at the mouth