Do you get audio over your SPDIF out from Windows normally (e.g. the Windows startup fanfare which is enabled by default in Windows?) There is no good reason why an application which normally produces basic stereo .wav type audio in Windows should not be heard equally well over SPDIF, so one approach to get things working is to tell applications like Quicktime that you are using two channel speakers or headphones.
You should be aware that Quicktime Alternative is not perfect, and also there are several possible different types of audio in Quicktime files.
An alternative approach to try is to rename the .mov file to .mp4 and use different codecs altogether to play it. For .mp4 you can use Haali Media Splitter, ffdshow audio decoder, and CoreAVC video decoder. If that doesn't work immediately then look at what audio renderer is being used (or ReClock) and try making changes there. I'm assuming the file you are playing probably has AAC audio (the most common in recent trailer downloads etc).
Recommended settings for ffdshow audio decoder version Dec 21, 2005 using SPDIF:
* Codecs should include at least "AAC codec" set to "libaad2". Other codecs here do no harm and may be useful in other situations.
* In "Show/Hide filters", "visible filters" in the right hand panel should include "Resample"
* In "Processing", the top three boxes should be ticked but not "Dithering"
* In "Resample", the "Resample" box should be checked, and settings should be 48000Hz, libavcodec highest quality, and "Resample Always" should be checked
* In "Output", "Supported output sample formats", only "AC3" should be checked and bitrate should be set to 640 for highest quality assuming your audio receiver/speaker system can handle the full 640kbps, otherwise use 448
* Also in "Output", try playing around with the various options in the "Connect to" box. For me it works best to set it to "any filter" so start with that setting first (which will gray out the 'Apply only to S/PDIF output' box but don't worry). I have "Allow direct-to-file output" checked also.