I've recently updated to 1.9 but I've been having a lot of issues related to lag due to chunks not unloading and I think this may be the cause.

When running the method:
chunk.unload();

On any chunk object, the ChunkLoadEvent is immediately fired. The effect of this is that every time a chunk is unloaded in a plugin - it's immediately loaded again.

If this is happening internally in Spigot this explains why chunks aren't being unloaded at all once loaded. Are you aware of this issue?