Tomas is correct in that Digger does not remember your settings unless you do the same thing twice, like updating your file every <so many> months.
However, with a little scripting you can create templates and specify that template to digger. I did that with my "Traffic_Lights" scripts. These script simply loops through a long list of countries and prepares a template to be used again and again.
I don't know if that's over your head, but it is some work-around.