For start try a basic query
Code:
SELECT qt.UserID, COUNT(qt.[UserID])/(SELECT COUNT([QualItemListTBL].[Qual Item]) FROM [QualItemListTBL]) AS Percentage
FROM QualTrackerTBL qt
GROUP BY qt.UserID;
Check what you get. When this is OK, then add UserDataTBL and set join conditions, but don't add any fields jet. This query must return exactly same result table as basic query.
The next step, set the filter condition (either using HAVING or WHERE). Users having qualification finished must be left out from result table.
As final step, add additional fields from table UserDataTBL, and add those into WHERE clause too.
With such approach, you can determine at which step your data get wrong (or don't get wrong).