Did you tell it to render as 32-bit deep, so it can have 8 bits alpha to old the transparency, and did you tell it to use theobject mask (or whatever they call it) to set things apart from the background?

Quicktime needs TrueColor+, not just TrueColor. If you keep it as TrueColor it'll be 24-bit and ignores alpha.

Something like that. I don't know the details for C4d but it's probably similar to rendering from others like Carrara when it comes to the image format and depth.