It seems that you can enter the same prop in both tabs but you will only get the one entered under the config tab when you insert a BOM.
Another quirk with Prop Tab Builder you may want to be aware of is its ability to add props. when you may not want them added. For instance if you open an older file that has a prop under the custom tab and you now have that prop under the config tab. It will take the config tab value and if its blank your BOM entry will be empty. If you go to the config tab and delete the prop, it will just come back when you reopen "summary information."
What I had to do was create another prop tab for each (part assy & dwg) that has no entries. Now when you start a part and select PTB you get prompted to select which PT you want. When you open an existing part SW dosnt assume you want the added props and should you want the PTB again you can choose. There is an option for "none" but that dosnt work.
There may be someting I am missing but this is my work around until further notice.