I had this problem yesterday when installing the full version.
So, I install it, say "yes" to importing demo version save games, pick the correct path for the demo (the default path), and finish installing. But, when I get into the game, none of my saves showed up. So, I go under the Aquaria folder in Program Files, and the Save folder is empty. So then I go to the Aquaria Demo folder, and to my great shock the Save folder there also appears empty.
Luckily, after a little tinkering around, I found that the save files in the Demo folder were actually hidden, and if I clicked this button that said "Compatibility Files", they showed up and I was able to copy+paste them to the Aquaria folder.
Just thought I'd share this in case someone else has the same problem. I'm using Vista Ultimate, if that makes a difference.