I assume you don't have NO_DNS set in the HTCondor configuration. In that case, when HTCondor tries to figure out the local hostname, it calls gethostname(). Use the `hostname` tool to determine what gethostname() returns. HTCondor will then try to obtain the canonical name by passing the return to getaddrinfo(). If that succeeds, the canonical name from the first result is used. The `host` tool may call getaddrinfo(); I'm not actually sure. You may need to pass the `-a` option or call `host` multiple times, since you said "frequently" (implying "not always"), which may mean that different DNS servers disagree on the capitalization.
In short: as far as I know, HTCondor doesn't mangle any of the results it gets from any of these look-ups. It's probably a good idea to track down where the occasional all-caps ORG is coming from -- it may be a sign of other problems -- but you should just be able to set SCHEDD_NAME to whatever the schedd name to work around it.