Hi Marc,
Are there any data partition constraints applied to this particular user's role (assuming not because you used a test user with the same role)? Other thought is that it could be the group which that user is a member of - that matches up to the permission groups on certain categories. Its possible that the user doesnt have permissions to the categories which those docs are in if thats the case.
Outside of that the only other possible thing I can think of is that the user set something in their preferences for KT search - there are some settings for the type of search, using natural language search (nls) or keyword search etc. Have that end user log into SDM and pull up their preferences, and you do the same on the test user you created. Compare the knowledge preferences.
Hope this helps,
Jon I.