According to the documentation (Chapter 14 in the Definitive Guide) when creating a custom theme you only need to override the files you need changed in your own theme. In actuality you need to copy all the files over. Not sure if this is a documentation error or a symfony bug.
To recreate: in a project that uses the admin generator create a new directory in data/generator/sfPropelModule/mytheme. Then in the generator.yml change the theme to mytheme. There is an error when run. If you copy the entire contents of sfPropelPlugin/data/generator/sfPropelModule/admin to the mytheme directory it works.