When outputting the Organization Relationship's System Record ID in Query and Export, the System Record ID's are different between the two functions for the same organization relationship record.
We are currently evaluating this issue.
Alternate solution: Export from the Query
Steps to Duplicate
1. Open a New Constituent Query 2. Output Relationships> Organization> System Record ID 3. Open a New Constituent Export 4. Output Relationships> Organizations> System Record ID 5. Compare System Record ID between Query results and Export results