Using 9.1.0 build in MC 1.10 (Forge 12.18.0.2000)
It appears that mechanical pipes fail to function after a server restart. I've tested this with all tiers and also just unloading chunks, but like I said above, it's only after a server restart. It doesn't appear to happen in a single player world though. They do work after you break and replace them.

If it matters at all: this pump does not have any upgrades in it and it connects to a farm valve from Forestry.

This error has occurred again under user EzR3aL for 1.10.2 forge 2065. This includes for all pipe types.

Can't reproduce this, tested in both singleplayer and multiplayer. Closing for now as 1.10 is not supported yet by me, I'll take a look later.

It effects all pipes and cables in Mekanism, especially on multiplayer servers. The code for the transmission of stuff is hard to find but I'm trying to spot the problem.

I can confirm I am having this issue as well.

I can confirm this issue, happens when chunk is unloaded/reloaded.
Using:
Minecraft 1.11.2
Forge-1.11.2-13.20.0.2315-universal
Mekanism-1.11.2-9.3.2.307.jar
MekanismGenerators-1.11.2-9.3.2.307
MekanismTools-1.11.2-9.3.2.307
omlib-1.11.2-3.0.0-100
openmodularturrets-1.10.2-3.0.0-158
dynmap-2.4-3 and dynmap-core-2.4-2082
worldedit-6.1.8
chunk-pregenerator-1.2

http://imgur.com/a/YtCko

This also happens with energy conductors, they do not belong in a network but conduct, replacing one will break the conductivity. The new conductor thinks it's in a one-block network.