Are you telling us that you loose quality? If so you are doing something more than what you describe above. A straight converion of .flac to CD by toast is a lossless process.
You can prove this to your self if you want. Do a round trip conversion from CD to flac and then back to CD. Start with any CD you like and then compare the audio files on the two CDs with binary file compare utility and see if they are not bit per bit identical.
(Macs ship with software that you'd need to compare the CDs. read the man pages for "hexdump" and "diff".)
You won't lose any quality by doing that... if it's a question you are asking. It's not entirely clear in your post if you are describing a problem or asking a question.