As of 7.2.0-0.1, the default universe is now VANILLA, not STANDARD. The default can be overridden with the, condor_submit local, configuration option DEFAULT_UNIVERSE.

Test this by not specifying a universe in a submit file and verify that the submitted job has JobUniverse = 5 (condor_q -long will help).

$ cat no_universe.job 
executable = /bin/sleep
notification = Complete
arguments = 86400
queue 1

$ condor_submit -v no_universe.job |grep JobUni
JobUniverse = 5

An advisory has been issued which should help the problem
described in this bug report. This report is therefore being
closed with a resolution of ERRATA. For more information
on therefore solution and/or where to find the updated files,
please follow the link below. You may reopen this bug report
if the solution does not work for you.

http://rhn.redhat.com/errata/RHBA-2009-0036.html