[Andrew Traweek]"My workaround has been to export into an intermediate codec I know works (like ProRes 422 or NTSC DV), then convert down to H.264 or WMV."
That's the way.
Try always to render to the less compressed options. Avoid DV if you can.
Set "Render in High precision" and "Motion Effects: BEST".
Try always to make a high quality/full-size master; from that one make the versions you may need.
Happened to me as well. I get a good chroma key on my preview but when you play the movie the key is bad. All items were in prores so it could not be the codec. This was very frustrating since everything looked good while settings were changed etc... but as soon as you play the movie its all gone.
My workaround was to switch the keyer from chroma key to something a little simpler, I think there was more than one option.