Eric Hoch mentioned the differences between Terminal an xterm running under X11. If you launch xterm with the command xterm -l (login shell), you will have exactly the same search-path as in Terminal. The default terminal which X11 opens is launched as xterm, thus the difference in $PATH. I added an xterm -l to the Applications menu, and use that for compilations, runnint LaTeX, xemacs (which broke under OS 10.4), etc.
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