My apologies for the delay in response here. I was on vacation when you asked the question and the email was lost in my inbox until now. I did solve this purely by luck. It appears that if you have conflicting privacy levels (and sometimes even not) the append will give different results. I turned off the following option in my reports and things stablized:
File=> Options and Settings => Options=> Privacy
From there I chose the other radio button option "Ignore the Privacy Levels and potentially improve performance".