It seems this bug is still happening as whenever I restart my server some of mekanism's pipes are no longer connected to other mod's blocks, while some are fine:

as you can see the pipes on the left are not connecting while the pipes on the right are just fine.
And it's not just pipes, at some point I had a quantum entangloporter connected to a capacitor bank from Ender IO, every time the server would restart I would have to re-tune the capacitor bank to output energy into the quantum entangloporter.

Minecraft: 1.10.2
Forge: 2183
Mods: list.txt

by chance is that reactor crossing a chunk border where the missing connections are at?

Here it is with the chunk borders, the reactor controller and pipes are indeed in a different chunk.

Yeah, no, that's not the problem here, other cables have no trouble staying connected and multiblock structures have no problem forming even if they're in multiple chunks.
All multiblock form just fine even if they're not in a single chunk.
It might be related to it in as much as if it hasn't formed yet when mekanism's pipes are first loaded it doesn't connect. But that's just the issue, You shouldn't have to replace the pipes for them to receive a block update. Other pipes like Ender IO conduits do it just fine.

so unless all chunks load exactly the same time you will have a multiblock structure that has not formed. major issues. always place multi block structures within 1 chunk

I have exactly the same problem on DNS techpack.
And everything is on the same chunk.
Waila puts me this message when I snicke :

Should be fixed in 1.11