No more alpha in exported QuickTime movie from Keynote '09

Hello
In Keynote '08, I create a slide with no background (None).
I add some text with some fancy text IN and OUT features.
I export using the Animation codec and the transparency option.
When I reimport the movie in another Keynote '08 file, it inherits the transparency of the imported file and thus everything is perfectly blended.
In Keynote '09 it is not possible anymore.
Even if I import an exported QuickTime movie from Motion with a transparent background, it is not possible to have a perfect blend, all layers are opaque.
Last but not the least, adding transparent files on top of each other in QuickTime player does not preserve transparency despite the fact that the Animation + transparency features are added in the files.
Thank you in advance.

Hey Gary - first off, thanks for your reply! I am currently forcing spotlight to re-index to see if that might help me out. After that I will try your suggestion and run a system software check.
I need a ProRes export as this is going to be combined with IMAG footage from a live presentation as well as additional video from an Arri Alexa. I want to preserve as much quality as possible so that there isn't a discrepancy in the final edit. Originally, I was rendering a small test to the desktop to gauge output quality of animations etc. I did go ahead and re-export a second time to an external drive, but it doesn't seem to matter as Keynote appears to initially render everything to the startup drive no matter what. The second export still ate about 15 gigs from my startup disk and I am unable to find any sort of temp files anywhere!
I am showing all files in Finder and searching around the ~/private/tmp folders to no avail. In the image below there appears to be a discrepancy in the size being reported by finder and the size I'm seeing listed in terminal...

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