This is most likely standard behaviour - basically, the driver settings provided in the printer object (Start-> Settings -> Printer & Faxes) are defining what will be send to the printer (except they show "Use Printer Settings" )
The application can overwrite this, so you have another printer options dialogue from the application.
If the printer object does not contain a colour option, you cannot set it.
If it is there you normally can select it, but the setting in the printer object is the one you always will get as default. So, if you want to have this always, you're most likely bound to set it there - as long as you have sufficient user rights to do so.
Also know, that if you switch printers inside the application, the printer settings will fall back to their defaults inside the application.
