I need a bit of complementary analysis here, because this is mechanisms that I'm new at, but, looking at the code of BuildCraft both on nightly and builder, I see the following in BuildCraftCore.java:

import buildcraft.core.network.PacketHandler;

[...]

@NetworkMod(channels = { DefaultProps.NET_CHANNEL_NAME }, packetHandler = PacketHandler.class, clientSideRequired = true, serverSideRequired = true)
public class BuildCraftCore {

And then in BuildCraftEnergy.java:

import buildcraft.core.network.PacketHandler;

[...]

@NetworkMod(channels = {DefaultProps.NET_CHANNEL_NAME}, packetHandler = PacketHandler.class, clientSideRequired = true, serverSideRequired = true)
public class BuildCraftEnergy {

which seems to mean that buildcraft.core.network.PacketHandler is registered twice. Experiments show that this is indeed the case, so we have a number of packets that are processed two times by the server. Just removing packetHandler = PacketHandler.class from BuildCraftEnergy.java fixed the issue.

Could anyone with proper understanding confirm this?

Reviewed lived by CJ, confirmed the problem. Will fix on nightly.