Well, it certainly doesn't mean you're not pregnant. If you haven't had AF, you're certainly still in the game. Most women don't get a positive pregnancy test until about the time they miss their period. It sounds like you ovulated later this cycle than normal since you haven't had your period and are still getting BFN's. In all likelihood, things will all become clear soon, and if not, you can go in for a quantitative HCG blood test.
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Exercise can certainly throw a woman's cycle off. The fertility hormones are fat-soluble, and without a certain amount of body fat (usually at least 17-20% for different women, though some require more), you won't be able to ovulate, or ovulation may be delayed. We think of healthy women as having nice, once-a-month cycles, and we think that anything else is a sign of something wrong with our bodies. In fact, healthy women generally have a body fat percentage quite close to the line, and many healthy, athletic women do not ovulate in what is commonly referred to as "runners amenorrhea." This is not a sign of pathology. This just means that their body fat percentage has dropped far enough that they are not ovulating but are still quite healthy. It is a normal, natural (though uncommon) state for women to be.
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As your body fat percentage drops, your cycles will become longer and longer and may stop completely. Having longer cycles will not necessarily be a problem for conceiving, but if your body fat percentage drops too low, it could be a problem. Super intense work-outs are not recommended for women who are trying to conceive because of this, and many women have found it helpful to conceive by easing up on their work-out schedule (while maintaining a healthy and active lifestyle) and allowing their bodies to increase their body fat percentage. I have seen some research that milk fat (whole milk, butter, etc) has been helpful for increasing fertility, but if you do this, I recommend getting the best quality possible since toxins are stored in the fat. Organic is better, grassfed is best.