I am not sure about it, but had the same issue with new eco-complete substrate more frequently than I had with aged eco-complete. Don't know if it was related to the fact that the substrate was not acid.
tom barr has mentioned auto fragmentation as the reason why some stemmed plants rot away only to search for better life. I like this theory however, what puzzles me is that i can snip off a well grown portion of a plant and place it with its parent plant and it will continue to grow up until a certain height where the bottom of the stem begins to rot yet everything else on the plant is in tip top shape. All the stems under a certain height is healthy. It's really annoying to be because every how and then i have to replant. I just rather just keep pruning. I tried placing the stemmed plants all over the tank and it continues to keep does. It might be a lighting issue but then again i'm grown HC and everything else in the tank is growing. Any help or is this just auto fragmentation as well?