After some more testing, it seems likely to be a bug in the Linux version of the standalone flash player. What happens is that if I launch the swf from a file browser, it loads the flash player at some default resolution, reads the height of the viewport and sets it as what 100% should be, loads the flash file, changes the resolution so the viewport matches the flash file's specs, and then reads the width of the viewport and sets it to what 100% should be.
The result is that the flash player's default window height determines what Flash thinks the height of the viewport should be, but it correctly reads the width of the viewport from the flash file.
If I load the flash file, and then click in the little 'URL bar' and hit 'Enter' to re-load the flash file (with the viewport already resized correctly), it works fine.
Wow thanks so much for the info! I'll keep that in mind if it happens to anyone else. I'm glad you found a workaround!
Someone was able to build the game for Linux -- they had some graphical problems, but I'm actually not 100% sure if it's a linux thing or a Radeon graphics card thing. A few other windows users have reported the same bug. It would be cool to have a native linux version of the game!