I know this was a issue b4 and i read that it was fixed. So i updated to 1.2.3C and let a Reed (dunno if it matters) fishing rod run down till it broke and the server crashed yet again.

java.lang.ArrayIndexOutOfBoundsException: -1
at mariculture.core.tile.base.TileStorage.func_70298_a(TileStorage.java:30)
at mariculture.fishery.tile.TileAutofisher.process(TileAutofisher.java:71)
at mariculture.core.tile.base.TileMachinePowered.updateMachine(TileMachinePowered.java:94)
at mariculture.core.tile.base.TileMachine.func_145845_h(TileMachine.java:100)
at net.minecraft.world.World.func_72939_s(World.java:2492)
at net.minecraft.world.WorldServer.func_72939_s(WorldServer.java:669)
at net.minecraft.server.MinecraftServer.func_71190_q(MinecraftServer.java:943)
at net.minecraft.server.dedicated.DedicatedServer.func_71190_q(DedicatedServer.java:423)
at net.minecraft.server.MinecraftServer.func_71217_p(MinecraftServer.java:798)
at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:658)
at java.lang.Thread.run(Unknown Source)

Dont know why that happens xD I aint a programmer :P.
If u need more info lemme know.