The reason why it is believed that if two mares are bred, only one will get pregnant is because of the variability in mares' bodies and the timing necessary. The January 1 birthday, outside the ideal breeding time, is not an effective time to breed. Since it is hard for some people to detect the heat, it can make the timing easy to miss. Some mares have "split estrus" or "silent heats" which can once again interfere with timing. Since the ova and spermatozoa do not survive well in the warmth of the mare's body they die quickly. Mare cycles varied quite a bit and it makes it hard to time the breeding with the ovulation. Bacterial Infections can interfere with fertility, as well as some inherited and gained traits. Good health and quality food will keep a mare in condition, but if the mare is not given the nutrition she needs, she may not be able to carry the foal to term.
In other news, while studying zebras I found it interesting that the alpha females were more fertile than mares lower in the pecking order. This may have a correlation to available feed, resources, and lowered stress levels for alpha mares.
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