..At least, that's my best guess as to what's going on here. I reproduced the issue with a fairly small setup but I haven't done a ton of fiddling with it otherwise.

Test setup:

The left chests are set to extract, always, purple and cyan channels respectively. The right chests are set to insert with purple, pink, cyan.

The left left chest is a Spruce Chest, right one is Dark Oak Chest. Both added by Quark. (the three right chests are obviously plain oak chests but this works for any inventory)

I deposit a stack of cyan and purple wool into the respective left chests (matching the channel color). Now let's look at the contents of the right chests:

Purple chest:

Cyan chest:

Pink chest is empty as expected.

My thought is EnderIO does not detect the different wood chests as separate, and instead is treating them as one connected chest.

EnderIO-1.10.2-3.1.156.jar
Quark-r1.1-70.jar
Pack is Direwolf20-1.10 v1.3.2.

Thanks for reproducing it, I've been without Internet today and it turns out Curse won't even launch without Internet, so I can't load my game. (posting this from phone). Nevertheless, I think I found the appropriate quark bug, see link above.

If they pretend to be vanilla chests, that's probably true. Vanilla chests always connect, so there's no way to ask them if they are connected or not. I need to check how to detect that for Q chests then.

Oops, I still had 1.7.10 in my head. In 1.10.2, the "chest combining" is not done by our code anymore. Now the chests do that themselves.

Can you test what happens with a hopper? So

(Chest A)(Chest B)
         (Hopper)
         (Chest 3)

Put an item into chest A and see if the hopper pulls it out.

With the following setup, the Acacia Chest is not above the hopper, but does lose its items to the hopper. Looks like an issue in Quark.

I even tested placing chests on all 4 horizontal sides of the chest on top of the hopper. Only one double chest forms at a time (not visually). Connections form East, then North, then West, and lastly South. (EDIT: though that was also the order that I placed them, and I'm too lazy to start up Minecraft again).

Minecraft 1.10.2
Forge 12.18.3.2209
Quark r1.1-70