I'm having the same problem as well, for all games, including default/included games, in 3.0 only, running on Mac OS X Lion. E.g.:
[LOG] The file /Users/username/stencylworks/games-generated/Catapult/Export/flash/bin/Catapult.swf does not exist.
The .swf file does not appear to be generating in 3.0. Version 2 still works fine, still generates test .swf files as expected, although I notice they go in /stencylworks/preview/ as "Game.swf", not in stencylworks/games-generated where 3.0 is looking for them.