efiction recognizes BOTH carriage returns and <br/> tags. My suspicion is that you've got both in there, so when the software looks at your chapter and shows it back to you, it doubles the spaces.
Erm... I have the exact same problem, but I don't use <br/> tags at all, actually. I have a suspiscion Infinitestarburst doesn't as well... Anyhow, the problem arises only when one edits the fic. If one doesn't touch the story once it's 'published', then nothing goes wrong with the spacing.