You know, yesterday, I had an irrational argument with my boyfriend about shelves in a closet (see how irrational it is?) and today I'm a pound less than I was yesterday.
I'm going to chalk up that ridiculous fight (he did nothing wrong except be there!) to the fat I was losing in the process.
On a more serious note, I break out when my hormones are out of whack but it doesn't have to be related to low-carb. It might be that your body is beginning to respond to less carbs, so you're not having the same blood sugar fluctuations that you were having before and your hormones are being affected in different ways.
I went through a period of that (even though I am not officially a low carber) recently when I lowered my calories and consequently had to lower my carbs (so I could maximize my calories!).