The following is based on a decompiled version of Minecraft 1.9 using MCP 9.24 beta.
The field net.minecraft.block.BlockRedstoneTorch.toggles is a map with Worlds (like Overworld, End and Nether) as key and a list of redstone torch states as value. The problem is that a world is never removed from this list, which means that all save files you load containing redstone torches that burned out have still a reference in this list and cannot be collected by the garbage collection.
In general it might be better to use a TileEntity to store this value. But I am not too familiar with what effect this would have on performance.