Are you using some sort of integrated security? The database server you are connecting to should have a log of the issue. It sounds like that your users are able to login to BOE, Correct?
My guess is that the users in question have access to BOE, Universe etc, but do not have access to the tables / views / Stored Procs on the database server.
Are some users connecting to the Java BOE and others the .Net version, are only the Java users having the issue?
Check page 268 of the BusinessObjects Enterprise Administrator's Guide . You can download it from Business Objects.