Anyway, my situation is that I'm making an intro for my channel using a Cinema 4D clip which I planned to transfer on Sony Vegas 12 to continue the edit.
The problem is simple: When I put the 3D clip from Cinema 4D, it is transparent and everything goes in front of it (It's not a layering problem from Sony Vegas, I have already edited multiple times with Sony Vegas.)
For exemple, If I try to put a background to the clip, the background is gonna appear behind the clip but we will see trough it. The opacity is at 100% so I don't understand what the problem is.
Are you saying the transparency on the C4D clip is not working correctly, like it isn't actually transparent? If so, you'll need to right-click and choose Properties, then tell it the correct alpha channel.
If this isn't your issue, then I'm sorry but I've never come across something quite like that. Good luck.