Here are the first few things that come to mind
- Did you clean and lube the gun according to the manufacturers recomendations before you shot it?
- Did you try more than 1 type of ammo before you gave the gun back?
- What kind of ammo were you using?
If it wasn't cleaned and lubed before you shot it, that could be the reason for your malfunctions. The other thing that sounds odd is that you said the primers on rounds that didn't fire had a good skrike mark from the firing pin. That would lead me to believe the ammo you were using wasn't so good.
It sounds like the shop is willing to help you out a bit by sending it back for you. I would stay positive until you have reason to worry. I'm sure the factory is going to give your gun a pretty good going-over and will test fire it before they send it back.
Be sure to post back when this gets resolved!