I think the problem may be that when a server-side script is run on LabKey, the credentials of the logged on user are used for the query. This is true even when using the Rlabkey package. The .netrc file is not used and instead the user information from the session is passed to Rlabkey.

You might try giving yourself the same access as the special user in the .netrc file and try to run the script again on the server.