Just to make sure, when you were issued the ticket the VS flight had a DL# listed instead, or are you saying you flew on a VS flight that happens to be offered as a code-share?

If your ticket shows a DL for the flight then yes you are entitled to MQDs, and you need to get DL proof that you bought the flight as a DL flight number. In the 2nd scenario though you don't get MQDs. Just having the flight have a DL number doesn't make it qualify for MQDs, it has to be ticketed as the DL flight number.

Edit: Didn't see your post farther down. Yes as long as your ticket showed a DL flight number then you get MQDs. One thing to make sure of is did the flight change between you ticketing and flying? ie a schedule change or something else that caused the system to rebook you using the VS flight number.