Values of Non-Qualifiers (lookups) not auto-converting.

Question

We've been trying to use Import Server to automatically import records (XML) that had data for qualified lookup tables. Apparently there is an issue with namespaces in both the schema that we mapped to and the source field.
After removing the namespaces, we now have an issue with the non-qualifier that uses a lookup table not automapping it's values and thus retaining the compound field at the Customer main level.
First, the Partner Function is mapped to the Partner Function flat lookup table. At this level, the value auto-converts and the green dot is visible to the left. 
Second, at the Customer Partner qualified lookup, the Partner Function is again mapped to the Partner Function lookup. This time, however, the values do not automatically convert and the "AUTOMAP" button must be manually pushed for them to map. The other non-qualifiers (CustomerID, PartnerNum, PartnerSAP_ID) are also mapped and their values auto-convert (green dot).
Finally, at the Customer main level, all of the non-qualified field from the Customer Partner table are mapped and all auto-convert except for the Partner Function field. This requires us to manually push "Automap". Then, and only then, does it allow us to right click on one of the fields and create the compound field to map to the Customer Partner field. Again, the value mapping is not automatic but must be done manually.
This map is then saved and ImpMgr closed. When the IM is reopened with the same map, the compound field is not recreated due to the fact that the Partner Function values did not convert. Once these are redone manually, then and only then can the compound field be recreated and value mapped.
When this same map is used in the Import Server, the error is that the qualified fields cannot be mapped. This brings us back to the lookup fields not value mapping. Likewise, if this same file is opened in Import Manager mannually, and the map applied, it STILL does not convert the values and the Compound Field for the Qualified L/Up table is dropped. 
We are using MDM 5.5 SP4 Patch 3.

Answer 1

Hello Christiane,
Yes, this is a very important point and I should have noted it in my original post. Yes, my Default Batch Handling settings are:
  Yes - Automap unmapped values
  Add - Unmapped Value Handling
Plus:
  Replace - Default multi-valued update
  Append - Deault qualified update
  None - Default matching qualifiers
Also, in my mdis.ini file, my settings are:
  Automap Unmapped Value = True
  Unmapped Value Handling = Add
  Always Use Unmapped Value Handling = True
It used to work when we were in SP4, Patch 2, but have since upgraded to Patch 3, Hotfix 2(?) and can't get it to work.
Thanks for helping!
Don