I have now been able to get straight answers from Ladbrokes. The graphical statistics in my Score affiliate interface were entirely messed up with incorrect numbers. Ladbrokes apologized for this but according to them amounts of the paid commission were correct.
In regards to the negative carry over, indeed a term that permits them to carry over negative balances in specific cases has been in their t&c since many years. Apparently the NCO was erroneously applied to my account after the platform change to Mexos but this has now been fixed.
The person I spoke to made a professional impression and I will be glad to promote Ladbrokes again due to the quality of their casino.