if a root is exposed to light, it will start to differentiate into a stem and no longer a root...
this may be something else, but this can and will happen as described, too. Along with extra opportunities for contamination, paper towel method often exposes roots to light. roots don't like light.. they will morph into stem and lose the ability to absorb water over time. (doesn't happen overnight, which makes me think twice about what i see in pictures here)
so, if you weren't keeping them dark before, do that in future.