I just discovered that XQuartz on Mountain Lion does some annoying things to my PATH, changing:
in a Terminal window to
in an xterm.
The duplicate entries aren't so bad, but moving the system directories in front of Fink's is annoying. Running
pathsetup.sh again doesn't change this, unfortunately. I came up with a script which lets me reorder the PATH by blocks and remove via a pattern match any items I don't want.