one key piece of information you didn’t provide was how much RAM was in your system. If you like car analogies – The CPUs are the engine and the RAM is the gasoline. You can have 8 cylinders of raw engine, but if you’re giving it a straw to drink gasoline with, it will only go so fast.
That said, 45 minute program in about an hour given that it is a straight transcoding job isn’t horrible. And yes, QT32 could be a problem.