I know from experience the pain of having problems with a brand new pistol and needing to send it back to the factory. It sucks! If you're like me then you get excited taking out the brand new pistol for the first time and it's a pisser when there are real problems with it. With other brands I've even had to send them back more than once, but, by the end everything has worked out.
You're right in contacting CZ and I have confidence they will sort this out. It's definitely a shame their computers were down which is delaying the return. This happens to all companies and it's the last thing they want, too.
Now, I have no personal experience with CZ support but I often hear and read good things about them.
Hang in there, CZ will make this right.