I'm experiencing the same. I closed the ligand Viewing Options window and couldn't get it to reappear, so I saved the puzzle, opened a new client and tried to load the puzzle I saved. The ligand is outside the protein and the loaded score shows as -81015.411. I was also using the default track.
I stupidly closed the client on my windows machine after saving my exciting score of 9758, obtained by nothing I understand. opened and can not reload save and like gitwut, my ligand is haging out outside the protein. also, now everytime I wiggle sidechains the whole ligand seems to move through space like the Gargleblaster spaceship! Third, every time I move or change anything, I have to reset the sliders after each shake, wiggle or other move to see the grid (but thanks to Susume I found the grid).
Lost in space
Skip
I banded both the protein and the ligand in place (zero length bands to space), closed the game and re-opened, and can tell by the bands that the protein did not move but the ligand did. So the game successfully saved and loaded the protein position and the band endpoints but garbled the ligand position during saving or loading.
I moved the ligand to various spots outside the protein, banded it there and closed and re-opened the game. The ligand keeps moving back to the same place (same score), but the band endpoints are wherever I left them. Moved the protein backbone, closed and re-opened; protein stays where I put it while ligand moves back to its usual weird place.