Perhaps this is because your shell executes export LD_LIBRARY_PATH=... in one of the startup scripts.
The launcher does not start them, so the variable is not set.
Workaround: write a small script that sets LD_LIBRARY_PATH and starts Eclipse (use exec eclipse if you want to avoid a useless process that hangs before Eclipse exits).
Alternatively, edit eclipse.ini and add -Djava.library.path=... after -vmargs
To verify that this works, open Help / About Eclipse / Installation Details / Configuration. The path should appear as a System property in the dialog box.
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