Custom Presets Don't Work

I can save a custom preset, but when I load it, it has no effect on the sound. I have to load default effects and tweak them every time. Is there a way to troubleshoot this and get it working properly?
Audition CC
Mac OS 10.8.2

I tried to recreate your problem rendering Quicktimes to Animation + Alpha, ProRes 4444 + Alpha, and just plain H.264 and I didn't experience any darkening in all three renders. 
The Quicktime animation codec is pretty ancient and hasn't been updated since Quicktime Pro 7.  ProRes 4444 (AKA 4x4) is also as good as Lossless and has Alpha with a Depth option of Trillions of Colors +.  I would suggest using that.  In the Output Module box where it says Video Output choose Channels: RGB + Alpha, Depth: Trillions of Colors+, Color: Premultiplied (Matted) with Format Options set to ProPres 4x4.

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