Flex's css stuff seems to freak out occasionally. I find
doing a clean build or a restart of the app helps. If not, then you
probably have some bug in your CSS that isn't obvious that throws
things off. Try removing each section of CSS until you see which
section is causing the problem, then narrow it down.
Also, keep in mind that assets are relative to their files
and that can be problematic at times, especially when going from
dev to production.
I generally have my folders look like:
I have my style.css in the assets folder along with my embeds
and I still include everything as ../assets/ because they are
relative to the src/App.mxml that they were included in as opposed
to the location of the CSS file I believe.