Actually, that path is invalid as well (at least under build 6.50.0 GA). I did however locate the checkbox under this path:
Window >> Preferences… >> MyEclipse Enterprise Workbench >> Files and Editors >> JavaScript >> JavaScript Source
The short path for finding this location was to simply right-click on the warning/error light in the folding column of the IDE and choose “Preferences…” from the context menu. Took me right to the same place…