I think maybe this is a problem with how you are define the units/army when you set the game up.
The best way I have found is to do this (some of this you may know!):
Before a game go to Edit - Army Templates - then select "new"
Below Units select "New"
It should pop up saying "10 untitled"
In Troop Type put in what they are lets say "Chaos Warriors" - the program should then change "10 untitled" to "10 Chaos Warriors" and "CW" should have appears in initials.
Now Click on "duplicate" and it will create another unit the same, now it will have changed initials to "CW1" and "CW2" respectively for the two units.
We're going to make #2 a special unit so in "unit name" type "Kurgan's Mauraders". This will change the in unit label to "KsM"
In "Template" (Army A) at the top left type "Chaos Warriors" and click OK. and close the army template editor. (if setting up a game you would want to define 2 full templates here, but this will do for example)
Now go to file - new
Where it is Army A click on define and in "army definition" screen go to template and select "chaos warriors" from list. Now go to "unit from template" at bottom right. Check "select all" and then OK. The 2 warrior units should have appeared.
Click OK on army template and OK on define armies.
Skip terrain phase and go to deployment. untick "in the box" for both Chaos Warrior Units.
You should now see the initials you defined "KsM" and "CW" inside the 2 units and "Kurgan's Mauraders" and "Chaos Warriors" above the two units. Note that the external label defaults to the "troop type", unless there is a "unit name" specified, in which case that is displayed as well.
The key is defining and saving the army template FIRST and then selecting this army template when defining the army in game. That way all the details stay on record and the armies can be easily used/modified for the next report.
Hope this helps!