First, I'm not a Dr. and second, my wife has not been on oral contraceptives for 3 years. All I know is what we learned in her quest for an alternative to the strong dose est/progest pill that caused her problems with complexion (Rosacia<sic?>). The last oral C she took was Orto TriPhasic. She tried three different 'mini' pills as they are called before she found one that liked her. I say liked her because what you described was what the first two were like for about four months each. Add to that depression and life was a roller-coaster around here.
But it was worth it! The triphasal mini pills were at that time the best in terms of minimal hormonal content and closely mimic the natural hormone phases of the body. I don't know if that is still true, but she needs to do the research to make sure. The theory was that the mini doses of hormones did not overpower the body and force it into submission like some of the more powerful pills. However, some women have endocrine systems that do not respond to the (relatively) mild prodding of the minipill. My wife finally found a combo and dose that worked, so all was relatively normal and predictable for two years.
The only down sides to the mini pill for her was that because the hormone doses were low, she was subject to break-through bleeding and some slight variation in cycles. This is similar to when she was on no contraceptive at all and stress and illness affected her cycles. She also still had the estrogen bloat and fat retention. But that is because she is hyper sensitive to estrogens, not necessarily the mini-pill. All-in-all, the mini-pill was great for her. <if you can call altering a natural body function using chemicals great
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Again, these are her experiences and your G/F's mileage WILL probably vary. Also remember, this was 3 yrs ago and the science may have changed, and my memory CERTAINLY has! Check the current state of research for yourself.
BE
P.S. Your observation about the three months is well noted. Also, have you ever noticed that it almost always takes six weeks for ANY musculo/skeletal injury to heal? I thing Dr's are too general with their generalizations!!