I started a thread on the PCOS board a month or so ago about the same issue. I have PCOS and am taking bc to get a regular tom (I had actually gone a few years without it-not that I'm complaining, but then needed bc because I became *active* <sigh> all good things come to an end!)

...Anyway, my first week on Atkins, I got it as expected. Then I got it 2 weeks later (week 2 of bc pills) which lasted 6-7 days. Then 1 week later (week 4 of bc pills) had it as normal, 4-5 days. That was last month, haven't had it since, expect to get it this week. I'm hoping it was a one-time-only blip.

A response on the PCOS board said that when you're "emptying" the fat cells, you're also emptying the estrogen in them too, which could cause the fluctuations.

Don't worry, you're not alone!!