You likely have anaerobic conditions in you raft. The area that stinks is not getting enough oxygen so you need to add aeration there.
Yep, likely anaerobic raft water, though cold water and slow growth can show the same results while being quite aerobic. Roots catch shit, and if the water is too cold for rapid root growth and proper bacterial action, they will keep accumulating gunk until the area under the surface becomes anaerobic, and stinks. It can stunt or kill your plants, so best to fix the prob.
Do you have any filtration of the water going from your fish tank to your raft grow bed? Failure to filter properly will result in solids building up on the roots and bottom of the raft tank.