The more I test it the more it seems like a limitation of what the software can do.
I did an experiment with 4096 commandblocks, I built them all in the same 16x16x16 Chunk just to make sure it's not an issue with it chaining between chunks and I'm getting one tick that chains through all of them, and two other ticks that chains only through about 1/8th of the way till the next tick starts, this happens consistently at a rate of two ticks that don't chain all the way and one tick that does, every 3rd tick goes through all of them.
The more I test it the more it seems like a limitation of what the software can do.
I did an experiment with 4096 commandblocks, I built them all in the same 16x16x16 Chunk just to make sure it's not an issue with it chaining between chunks and I'm getting one tick that chains through all of them, and two other ticks that chains only through about 1/8th of the way till the next tick starts, this happens consistently at a rate of two ticks that don't chain all the way and one tick that does, every 3rd tick goes through all of them.
Here's a log that shows this behavior.
http://pastebin.com/zi1dFCKG
The recipe was removed, the item itself wasn't, you'll be able to find it within random loot in:
Villages/Dungeons/Mineshafts/Strongholds.
It can no longer be crafted, but it can be obtained through exploration.
I reckon it's because of this behavior that what's seen in
MC-90257happens, regardless of chain length.