I'm having a similar but opposite issue. Did you ever get a response to this post?
I understand there is a one-to-many relationship with programs (i.e. one lead can be a member of many program). That said, when I try to run a RCA Program Revenue Stage Analysis - ONLY leads originally 'aquired' by the program are counted. Therefore my MQLs per program are super low (becuase many leads are alredy known to me and in my database).
I can workaround this by running multiple reports in Analytics, but, I'd prefer to run 1 report in RCA. Is anyone running MQL reports in RCE?