Export a self contained QT using Export>>QT Movie, then use that file as your master to make whatever other file types you need. If your timeline is fully rendered Export QT Movie is very fast, and your other encodes will go much, much quicker too.
What happens if you dont use Quicktime conversion but just export a Quicktime movie ? That should be fairly speedy as long as your timeline is not hours long.
Then use Compressor to create whichever flavour or Quicktime you need ?
If you are not sure about using Compressor you could download something like MPEG Streamclip which may suit and is a little simpler to use.
Hope that helps
Ah David gave same advice while I was writing this reply,
that the way to go for sure.