Dear FedUp: The easiest question first, OK? There is unlikely to be any linkage between being Rh- and the variety of problems you have been having with your birth control pills. In terms of your specific problems (breakthrough bleeding, skipping periods, pregnancy type symptoms) here are some of the most likely explanations.
1. Breakthrough bleeding---Breakthrough bleeding (BTB) can be a common side effect of most types of hormonal birth control (eg pills/patch/ring/shot/Mirena IUD). Among birth control pill users BTB frequently occurs after a missed or late pill. In your case it sounds like you are careful to take pills at the same time daily. More remotely, BTB in a pill user can arise if she has gotten a chlamydia infection. Yet, if you both are monogamous this is not going to apply. If a woman has fibroids (more common in one's 30s and older), or polyps in the uterus that can make increase the risk for BTB.
When a woman uses hormonal birth control it can make the lining of the uterus more unstable--so it is easier to have some of it begin to shed. Sometimes the lining is less stable because the hormones make the lining much thinner (actually this is good as a thin lining is a healthy lining). This reason is more common in longer term Pill users. Sometimes the lining is unstable because the hormones can make parts of the lining out of synch. This is more common in new users.
2. Absent periods on the Pill--Birth control pills are formulated to keep the lining of the uterus thin. This is be sure that "Pill periods" are lighter and as a protection against cancer of the uterus. The downside is that, over time, the lining can get so thinned out that there isn't much inside to shed.--causing super light or missed flows. It is also possible for a woman who misses "Pill periods" to have such a thin lining that it is less stable and prone to BTB.
3. Pregnancy type symptoms--Some women will have nausea from the Pill. This is most common in higher dose pills and new users. Taking the pill at night with a little food can help this. Some women will note breast tenderness or enlargement. This can be due to the hormones in a specific brand of Pill.
Bottom line, BTB on hormonal methods of birth control is a nuisance side effect. The protection from pregnancy is still in effect. If your poor cycle control persists you should keep going back to your GYN or clinic. Often a change in the brand, or formula, of birth control pill will fix the problem. Honestly I have had some women patients who could take any Pill and have no problems while others tried multiple formulas/brands to find the one that worked the best for them.
In Support,
Jane