Originally Posted by flyerCO

The agent likely has your KTN on file and thus adds it. You can search past threads that deal with DL and KTN issues. They document the same thing. The KTN from your SM profile is only added if you book with DL. If you book elsewhere then it must be added. This can include, if it's in your profile with whatever TA during booking. When work books a flight for me (instead of me booking myself directly with DL) my KTN is added. However this is because they have my KTN on file in their profile for me. It shows up even if there's no FF attached (ie when booking an airline I don't have one to use). If customer books flight directly for me, even if they include my SM number, my KTN doesn't show up, unless they book directly with DL.

Basically your profile with whomever you're booked through determines if it gets added. If booking with DL, then your DL profile. If booking with a TA, then the profile on file with the TA.