TLDR: Crate makers say they make a crate every 3 seconds. I've timed it repeatedly and they are taking 10 seconds. So instead of needing 1 for every 3 refineries I need 1 for each refinery. I timed the furnaces and combiners and they all work exactly as they say making a package every 9 seconds. I can't imagine why the crate maker would make them over 3 x slower than they say they do.

The whole story WITH MATH!

So for example I have a crate maker which says it makes a crate every 3 seconds. Then I have a refiner which takes 9 seconds. One would think you could run 3 refiners off of a single crate maker if you worked out how to move the boxes around efficiently. So I build a huge mega factory with 14 crate makes supplying 28 refiners. That's only a 2/1 ratio instead of the 3/1 the math says should work. Then I set up 14 combiners because they say they take the same amount of time as a refiner 9 seconds. I only needed 1/2 the number of them since they are taking two refined mats and combining them so 2 refiners for each combiner. Hope I haven't lost anyone yet.

I even have farms. A farm with a greenhouse makes 6 mats every 45 seconds or one mat on average every 7.5 seconds. My bottleneck in the factory is the refiners which again I have 28 as that is all that will fit side by side across a 20 block factory (max size). So since that is the bottleneck of the whole operation (something had to be) and they process one material every 9 seconds 28/9 =3.11. So I need 3.11 mats every second to supply them. So if one farm makes one every 7.5 seconds I need 7.5x3.11 = 23.33 farm. Obviously this must be rounded up to 24 farm with 12 of green grass and 12 of red grass. I built 26 for good measure.

After countless hours (i could count them but don't want to) I have all this setup and running it doesn't work :(. Every individual process in the chain works perfectly. I have containers in the factory all linked together for each material type as well as they are all linked to the boxers they supply. In total there are 280 raw materials of each type of grass available to the boxers. These are being feed from outside but suffice it to say that these containers stay full all the time. However once up and running my tanks holding the refined mats coming out of the refiners stay empty. In general this would be fine, a proof that everything is perfectly balanced but thats not the case. I disabled my outputs and allowed these tanks to completely fill then turned them all back on. These tanks drained rather quickly.

I investigated every item and all I could find seemed to be working as expected with two exceptions. First, most of my refineries say they produce 1 in 9 seconds. One of them says 1 in 8 seconds. I tried timing them but can't be sure they both seem to be 9 seconds. Still why would one of them even say 8 seconds? I can't find anything about it that is hooked up differently than all the rest. The factory is water cooled but i can't see how that would affect one item and not another. The water tank is at 32 / 40 usage no not like its over max and some items are overheating while others are not.

Still thats not the worst of it. The crate makes all say "produces 1 in 3 seconds" yet when I time them they all take 10 seconds to make a box, WTF! Needless to say this is what threw off all my calculations. So instead of needing 1 crate maker for every 3 refineries you actually need just over 1 each. Or for my setup with 28 refiners I would need 32 crate makers to keep up. Or rather since 32 crate makers wouldn't even fit side by side I suppose I'd have to go with 1:1 ration and just accept a 10% loss in max production plus another $210,000 of build cost.

Anyway I've rambled long enough, maybe I'm taking this too seriously but there is a lot of number in this game and it would be nice if the math added up. Can you imagine if the math didn't add up in real factories? I'd love to know if this is a bug or some game mechanic. I thought it might even be related to lag but in testing every other component did its job in the specified time so I don't know why crate makers would be any different.

I wouldn't have thought that this could be the issue, unless you have unusually long arm rails or something, but crate makers also have a limit to how many crates can exist in the world at once. If there's 30 out from one maker, they can't make another until one of their crates leaves the map or is destroyed.

Refiners also have different speeds for different resources, just like the mines, but you can't tell unless you click on the machine while it's processing the specific resource. Which really sucks for ratios since the 1 crate maker to three refiners thing doesn't even work for most resources anyway (though I think only one resource is 1 in 8 seconds, so for the rest 1 crate maker to 3 is still as close to ideal as it's feasible to get anyway).