Hello,
Are you certain your batch daemon is running?
What is the output of:
# /etc/init.d/kaltura-batch status
Also, what do you see in /opt/kaltura/log/kaltura_batch.log and /opt/kaltura/log/batch/convert*log?
I am also a bit confused by your description above. Partner 99 is, like you stated, the KMC template account. It is not meant to be used for uploading entries or any other actions, apart from defining the template. When a new partner is created, it inherits partner 99's set of definitions.
Did you create a new partner from the admin console are using it?
Thanks,