OK, choosing the UT Video RGB option seems to have reproduced the colour faithfully to what I had in the project. Would it cause any problems if I used that for the final encode?

Also thanks for the help with how to choose a different codec in Premiere. It looked like the Microsoft AVI option didn't support HD but I was able to change the resolution once I chose the UT Video codec. Having smaller lossless files will make everything much easier. And unlike the previous lossless files, my computer is able to play these without stuttering! Awesome! Why couldn't I have found out about this sooner?