How likely is it that my brown, flaky discharge is just spotting. it's my first month on seasonique (i am on week 6 now) we use condoms every time.

I think it is: likely that your brown, flaky discharge is old blood/spotting. Seasonique is a combination oral contraceptive pill containing both estrogen and progesterone. Especially early on, there can be alterations in the balance of these hormones and spotting results. I wouldn't worry about this..if bleeding becomes more intense or persistent, review with your prescribing Doctor. Good wishes:)