RIP the best redstone feature in making deadly, compact traps; compact BUDs; etc... 😞
@Jesper I think the problem is that the redstone isn't sending the information to update in time before it unloads, because you can walk out of render distance and it will still run fine when you come back, but just jumping out of render distance is the problem. A long-term solution for Mojang could be having redstone, repeaters, comparators, torchs, etc update whenever it's chunk is loaded, though it would cause lag when rendering redstone-heavy chunks, it would fix this problem.
Or cause a delay before unloading a chunk to, like Jesper said, store where the update should be, but, again, lag is an issue here with chunks with a lot of redstone, and having a lot of chunks loaded at one time.
I am not sure about any other bugs that would come because of these aforementioned possible fixes, because I know nothing about Java and the Minecraft coding, but who knows?
In 13w02b, I have this problem, except when the chunks load for the first time when loading up the world, my redstone clocks would all stop, either on when it is a short clock, or off when it is a long clock (I use purely repeater and comparator clocks)...
I think this has to do with how the game freezes redstone when the chunk unloads, and it doesn't update when it reloads...
A temporary fix until then would probably be attaching a comparator from the newest snapshot to the area where it happens, since they give constant redstone updates to the block it's pointing at.
I do know that lag will affect block updates, as my desktop that my sisters have in their room (don't ask, its mine), when they run minecraft with the dozens of other background programs they have (I seriously regret getting a TV in my room...), their framerate is less than 5-6 fps on low render, regular lighting, etc. (you get the idea) and fluids, gravity blocks and redstone won't update reliably, or not even at all.
(Sorry about the ranting... my sisters seriously messed up my desktop. They even admitted that they get the Blus Screen of Death (windows crash screen) every day)