In Booking Manager you are able to choose whether you want to exclude Agency commission from VAT or not.
This option is located in Preferences > Reservation settings > Invoice. Just find the option Calculate agency discount without VAT and place check on it (1.) and press Apply (2.).
This function was introduced to enable you to either with calculate commission with or without VAT. This was not flexible since you could work one way or the other so you had to turn the option on or off.
Booking Manager v 9.0 has taken this option a step further and added the flexibility to set this option at the individual level.
Now the setting in Reservation settings works as a set default value, but you are able to go to your agent contact in the Address book and set the value for each agent individually if required
Open the Address book, find the contact (1.) and press on Misc (2.) tab. Now find the option called Agency discount without VAT (3.). Here you are able to select whether this agent will have his agency commission calculated with or without VAT, or will it use the default setting (4.) from Reservation settings.
Press Apply (5.) when you are done.