Just out of curiosity, was the Agent job running the TSQL commands you specified directly? Or was it executing a backup task via a Maintenance Plan? I've recently seen perfectly fine Maintenance Plan tasks start exhibiting odd, unintended behavior. Deleting and re-creating the Maintenance Plan task fixed the issue. I've learned through that experience that it's better to executing the backup action through the job directly or, even better, create some DBA stored procedures and then execute the sproc through a job.