Hi,
Good that it solved your problem..
With your scenario, I can explain it since you only have 1 exception aggregation..
Since you have this data..
1. Count of Confirmation - COUNT with exception aggregation SUM reference characteristic is Confirmation
2. KPI1 - Qty/ Count of Confirmation (Standard Aggregation)
3. KPI2 - insert KPI1 with exception aggregation SUM reference characteristic is Order
What your KPI2 does was compute the values as if ORDER is the only CHAR object in layout..So you have something like this:
Afterwards, KPI2 just SUM the values based on the layout given in your query..
Hope you understand my explanation.. 
By the way, just a trivia, EXCEPTION AGGREGATION works like CALCULATION BEFORE AGGREGATION before in 3.x..
Calculation After and Before Aggregation
Regards,
Loed