Is it a flood & drain system? If so, you might need a longer cycle - most references seem to go with 15 minutes. I was at a university aquaponics farm this fall, and they figured that it's not necessarily wet roots that causes the stems to decay, but a lack of O2. They pump pure O2 into thier systems and EVERYTHING grows like mad!! Doesn't matter if it's in F&D, DWC, Constant Flow - pure O2 does the trick!

Of course, most of us don't have the resources to run pure O2, so we have to do what we can to increase O2. 15 minute cycle in the F&D GB, aeration in the FT, etc.

With the leaves and fruit rotting when it's in contact with the rock makes me suspect the water is coming quite close to the top. You may need to add another layer (1/4-1/2"); however, it may also correct itself with a longer cycle.