The female estrogen cycle is very sensitive to the environment it operates in - i.e. the female body. The body will regulate such that it is only operating while there is a perceived "safe" environment for conception. So examples of when it may disappear are when bodyfat is very low, like during a contest prep (for me, typically around 11% bodyfat), too low for "safe" carrying of a fetus, or when there's a lot of stress (also had mine disappear for the first semester I moved away for college - very high stress). Similarly, the presence of hormone manipulators like AAS. So not knowing if you were dieting down during your cycles, it would either be from low bodyfat or presence of the AAS.
Also use of birth control regulates, and sometimes "promotes" estrogen (but in a controlled manner) - depending on your BC, it promotes estrogen effects such as water retention and estrogen-pattern fat depositing. So the combination of a cycle + BC is like two opposing forces trying to operate at the same time - they don't directly interact, but rather while the AAS is promoting lean bodymass (and depending on the substance, possibly also dryness like winstrol does - has an anti-estrogen effect to it) while the BC is promoting those estrogen things like water retention & bodyfat - so the end result is not as great leaning out of body mass etc.
This is why many competitors opt for an IUD as a non-hormonal method of birth control. (Technically Mirena has a slow-release progesterone in it, but otherwise is non-hormonal).
