This happened to us as well. Since everything in Altiris is stored in its SQL database, as long as you can get access to the SQL database, fixing this is a simple task. Please note that the following code is for DS 6.9, and we run our database on a full MS SQL 2005 server, so if you have a different setup, YMMV.
--This code will lookup the task_id of the DAgent Upgrade job and set the on_fail code to 0 for any job with that task_id in on_fail
update task
set on_fail = 0
where on_fail = (select event_id from event where [name] = 'DAgent Upgrade')
I hope this helps someone out there avoid having to do a lot of manual work to fix this.
Regards
Jason W