They do look to have rotted for some reason. Did you check out the roots? The tops of those look like they could be rotted too. The only sign of a pest that I could see was what look like shed aphid skins and it doesn't look like something aphids would do. Yes, I too would like to get them under a microscope. A good 10X magnifying hand lens is the next best thing and a lot less expensive.
Is there a pattern to the problem? That is, did it start in one place and spread out from there or are the affected ones scattered throughout the bed? Does media in the elevated bed get very hot, and does the moisture level fluctuate?
