My system is on SQL 2005, you may not have the same issues with an Oracle DB: JDE recreates the package specs DSN at every run and it was stuffing it up in ODBC setup, hence it would not build the specs at all.
Simply fixing the DSN manually had no effect, because it would recreate it incorrectly at every run. So I ended up fixing it in ODBC and then setting the security on the Registry to prevent JDE from breaking it again.
Oracle database access in JDE does not use ODBC, so this one would not apply to you.
And there were some other issues there too, which I can't remember any longer what I did, sorry. I think, the Package Build History was wrong: everything would be reported as perfectly successful, despite no specs were built, or something like this.
It's good to hear it worked fine in your case!