Josh M, welcome to the forum, and sorry you are having issues with your Vanguard.
I have a older Weatherby in 300 Wby, and I have never had any issues with mine. Let me ask you a couple of questions.
1. Have you done a thorough cleaning of the your rifle?
2. When did it start doing this? When you shot reloads and with factory ammo?
3. When you work the bolt, what happens to the case? Does the case stays attached to the bolt, or does it get ejected at all?
4. Have you thought about filming what it's doing and posting a small video here?
Not seeing what's it's doing, I can only speculate. But, it seems like the plunger is either dirty, or damaged. I'd call Weatherby again, and explain to them or maybe even show them the video, and I am sure that they will get it fixed and make you happy. Their customer service is great, actually it's outstanding. I hope someone from Weatherby see your post here. Please don't give up on Weatherby, reply to my questions, and hopefully we'll get it worked out.