While it's vaguely possible that microwaves could damage foods in ways we don't know about yet, the notion that water can be changed by a microwave is complete hogwash. There are very few things that can be done to water. You can contaminate it or decontaminate it. You can change it from ice to water to steam. You can turn it into oxygen and hydrogen. That's it.

I'd guess that, assuming that the experiment wasn't contaminated in some way, which I'm inclined to say it was, the microwave likely had an effect on preexisting contaminants in the water. Given how much easier it is to boil water in a microwave than on a stove, I bet the contaminants were simply more concentrated in the microwaved water. A good way to test that would be to start with distilled water.

I also bet the same vessel was not used to contain both doses of water. The only thing I can think of that can perform on the stovetop and the microwave would be Corningware, but I bet metal was used on the stovetop and either glass or plastic in the microwave.

I'd try it, but I'm terrible at growing plants, and, well, I've got better things to do than spend that much time disproving crackpot theories.