Open terminal and:
defaults write com.apple.dock no-glass -boolean NO
(Everything will disappear and reappear after #2 - if you get a permission error, you may need to type "sudo" in front of those commands and enter your system administrator password).
It's just the non-glass dock, though how it changed is odd.
Otherwise, the raw files are in:
They are called:
But I doubt you'll need to go in there, the 2d dock is build in just as the 3d, the terminal command should toggle it.