MDM hierarchy map issue - mapping not correct

MDM Hierarchy map issue:

We have a 2 level hierarchy import map set up for hierarchy reference tables. eg. company code/reconciliation account, company code/accounting clerk. Through Import server the mapping was happening properly and MDM is getting updated. But if the data is checked through Import Manager value maps are wrongly mapped. Why there is different behaviour for MDM import server vs MDM Import Manager. Flat tables we dont see this behaviour.

Please let me know your thoughts.