There is no "Downloaded Transitions" directory-- only the other ones.
However, with the EffectExtractor, it was interesting. The one I had installed was from 2010, about 500K in size. So I followed the link you provided and installed that version, which is date 5/13/2014. Still doesn't work, but I wonder if this is still not the correct version. I just purchased, downloaded and installed this software 24 hours ago, from CyberLink. I cannot imagine, for the life of me, why there would be an old version of that file. But, apparently, there was. The only other CyberLink product I had on my computer was their DVD player. Perhaps that file was already there and the installation, for some reason, didn't overwrite it.
Here is the info on what is now there from the link you gave me:
EffectExtractor 5/13/2014 8:41 PM Application 960KB
EffectExtractor.exe.manifest 2/26/2013 4:48PM MANIFEST File 2KB
If I understand correctly, the importing of transitions is new to PD13. If that's the case, it looks to me like there's a bug in their install which doesn't install the EffectExtractor if there's already one there, or something like that. Can you tell me what the info on your install looks like? Anyplace I can get the most current version?