It turns out /etc/profile and basrc are insufficient for GUI apps. You have to add stuff to some plist for system-wide paths.

Anyway I needed ndk-build in my path for Eclipse to auto-build my JNI/android code, so I created this file:

chef:jni vijayp$ cat ~/.MacOSX/environment.plist

<?xml version="1.0" encoding="UTF-8"?>

<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">

</plist>