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Custom Report Type - Why is it filtering out some records?

First, I created a normal Report based on Opportunity. However, I wanted to change the name on one of the columns. I read that the only way to do this is by using a Custom Report Type. So, I created a Custom Report Type  with just the handfull of Opportunity columns I needed. Then I created a Report based on this Custom Report Type. The problem is, the resultant report seems to be filtering out hundreds of Opportunity records. (i.e. the records don't display when I run the report) My first thought was the problem has something to do with the Hierarchy Level setting. Report based on Custom Report Type, the default is "checked". For the Report based directly on Opportunity, the default is "unchecked". 


For the  Custom Report Type - Report, I tried to uncheck the  Hierarchy Level and save, however when I try to edit again, the  Hierarchy Level has reverted itself back to "checked".


I am System Admin and am trying to develop this report for non-system admin users.