1) What happened
Custom shaders aren't exporting to flash.

2) How can we reproduce it using the example you attached

1. Create a new unity project in 3.5 beta 6.

2. Browse the asset store and download/import the "Ecosystem Generator".

3. Open the example scene.

4. Hit play in the IDE and notice how the flowers move. It's a custom shader, a minor change to the nature leaves shader.

5. Build and set the platform to flash.

6. Open the exported swf and you'll notice the flowers aren't moving.

Looks like it didn't export the custom shader and used the fallback.