Jobs run under the SQL Server Agent process, which is running under the domain account. Just because the job is owned by 'sa' does not mean it is actually running as the 'sa' account.
When you say the job is running on both systems - how exactly are you running something on the other system? You have already stated that you are not using linked servers, so - what is the command that is running on the other box?
Jeffrey Williams
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Managing Transaction Logs