Stop using QuickTime. That's what's causing the shift.
Quicktime has become an industry standard and a lot of times the decision to use it for delivery happens long before it arrives in my hands. I've requested and suggested every format known to man and I still mostly get Quicktimes delivered. My experience has shown that most people making decisions at a media distribution company have very little technical knowledge and "Quicktime" is synonymous with "digital file". It's unfortunate.
That being said, are there any known workarounds when you're stuck using Quicktime movs?
Try transcoding from AME or compressor before bringing the file into Encore. I'm not suggesting this will fix it; only wondering if there is anything different about the Encore transcode itself.
The QT gamma shift is fairly well known, but I don't use QT and don't recall what workarounds are successful.
Quicktime has become an industry standard
Agreed. The way to solve that is for companies to stop accepting them. The client want's your services. They'll send you what you need, especially if you send back the QT and tell them it just doesn't work.