I have heard that women who have very low body fat run the risk of their periods ending entirely, but I hadn't previously heard of a link between low-card and this type of disruption.
Personally, I've tried low-carb diets three times now - and I couldn't stick with them for more that two weeks at a time. I didn't notice any issues with my cycle, but each time the lack of energy and the dry heaves really did me in! Not to mention I didn't loose a significant amount of weight. Never again!!
I think that everyone reacts to extreme diets differently. For some people a particular diet protocol will work really well, while for others the same diet plan will be a disaster. You just have to find one that works for you.
In your case, if you've noticed a significant change in your cycle, I think you should discuss this with your doctor (or other medical practitioner). To me, no amount of weight loss is worth risking a potentially long term health issue.