Kelly,
can you check the install doc? it still references a dojo.js.uncompressed.js file that no longer exists, and references the [HOSTNAME...] which also doesnt exist.
Do we need to do anything to localize the file?
Also, in both init.js files for 3.1, there is serverapi.arcgisonline.com/jsapi/arcgis/3.1compact/js/dojo/dojo instead of expected [HOSTNAME_AND_PATH_TO_JSAPI]