Why microwaves do not kill harmful bacteria as well as boiling?

I'll go ahead and take a stab at answering this, even though the question is a bit vague. I assume by "cook" you mean "cook with a non-microwave method", like boiling, steaming, baking, frying, sauteeing, or anything else.

First of all, no, I can't think of any reason why microwaves would be worse than any other cooking method. If you fully cook something in a microwave, it is as safe as fully cooking it any other way. If the food reaches the same temperatures, and is held there for the same amount of time, the bacteria will be just as dead no matter what the heat source is. The heat supplied by a microwave is fairly similar to that supplied by steaming, and no one claims that steaming is an unsafe cooking method. The only thing I can think that would be unsafe is if you don't actually fully cook the food, but just heat it to the temperature that you want to eat it at. But that'd be a problem for any cooking method; dangerous undercooked meat is dangerous because of the temperature, not the cooking method. (And of course, not all food needs to be cooked to be safe.)

The arguments you suggest don't really make much sense to me, either. For the first, I don't have any idea what you mean by heat frequency or sequentially different waves; heat is not a wave, so I'm not sure how to respond. No matter how you're cooking something, heat is being transferred into the food. Heat caused by absorption of microwaves is no different from heat supplied by contact with boiling water, steam, pan, or the hot air in an oven. It's still heat transfer, and it makes the temperature go up. Different methods may heat more or less evenly, or at different speeds, but heat is heat.

As for your second suggestion, reflection of microwaves, well, that happens already. You may have noticed that the food in a microwave ends up hot on all sides; this is especially noticeable if it's a big solid piece of food like a casserole. It'll be hot on the top, the bottom, and the sides. The microwaves are reflected around; there's really no other way for it to be. If they weren't reflected they'd have to either be absorbed (meaning your microwave would heat itself up) or pass through the walls (meaning standing next to a microwave would be dangerous). And it'd be horribly inefficient, on top of that.

Of course, all the stuff about reflection and heating from all sides is still a moot point in terms of food safety. When you cook something in a pan on the stove, as long as you fully cook it, it's fine, even though it's only being heated from the bottom. All that matters is the temperature the food reaches.

Microwave ovens do not cook food very evenly. This is improved by the turntable, but unless the food is stir-able and you stir it, the food will have hot and cold spots. Most people seem to overcook food and then let it rest for the heat to even out

Most other cooking methods are slower than microwave cooking, so this give time for heat to conduct through the food and give a generally even heat that given time will render most surface bacteria safe (not that you should rely on this). With microwave ovens, the high speed of cooking, the uneven heating, and also insufficient time for heat to conduct through the food without seriously over cooking your food, means you cannot rely on this

You should not cook food that requires heat to kill bacteria, it is always a non-perfect process, regardless of the equipment you use so it is risky, microwave oven or not

There's an interesting article on The Straight Dope that tests the question of how well a microwave kills bacteria on pizza. Here's a few quotes:

If I take a piece of pizza that's been sitting on the table awhile and microwave it, would that kill the bacteria, or am I just eating nice hot bacteria?

Will a microwave kill microbes? Sure. Microwave ovens use electromagnetic radiation to heat water molecules in food. It's the heat, not the microwaves, that's lethal here; the hotter you make your food, the more likely you are to kill the bacteria in it. (Some contend microwave energy itself is fatal to bacteria, but that's unproven.) The key is making the food hot enough uniformly enough for long enough. If it heats unevenly, a common problem in microwaves, some bacteria may survive.

After running some real-world tests and examining their petri dishes, they concluded:

1. Heating the pizza for 30 seconds was relatively ineffectual.

2. Heating it for a full minute killed most of the bacteria but not all.

3. We didn't go in for another round of testing, but suspect that at least two minutes of microwaving would be needed to ensure 100 percent bacteria eradication, at the possible cost of rendering the pizza inedible.

Checkout the full (quite entertaining) article here:
http://www.straightdope.com/columns/read/2947/do-microwave-ovens-kill-bacteria