If you put a line of adjacent command blocks to be executed at the same tick, they are not activated in the powering order, firstly powered (strongest power) firstly executed, they are instead powered in some situations that seems to be unique, here what I've seen :
the same system in two different worlds at the same position does not change activation order, should does like now.
the same system made at the same position, with block at the same position but with blocks placed in a different order does not change the activation order, should does like now.
the same system in two different position (in the same chunk) change the activation order, should not.
the same system at the same position depending to chunks but in different chunks change the activation order, should not.
the same system with a different rotation change the activation order, should not.
the same command blocks at the same position but with redstone source at a different position change the activation order.
If we additionnaly put command blocks around the directly powered block, they should be activated depending to their relation with the directly powered blocks (always top > north > south > east > west > bottom for example)
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Please force a crash by pressing F3 + C for 10 seconds while ingame and attach the crash report here.

This crash report has been manually triggered, not triggered at the same time the screenshot was taken, but the same world, position and condition has been reproduced.

That's fine. Please attach it.

Confirmed.

See here (http://www.youtube.com/watch?v=Zt7YEYdx6RE) for an explanation of what is likely causing your issue. Redstone is not updated in a systematic fashion like other block updates are, but instead utilizes a HashSet of locations that need updating. This set is highly dependant on the coordinates of each and every block in the system, so translating or rotating the wiring would cause the set to be iterated in a different order.

Isn't this a duplicate of MC-11193?

@Torabi : No, the way CB and Piston update is very diferent from repeaters, If CB could acte as repeaters it would be a real step for this problem.

At least related to MC-11193

The difference between command blocks and pistons isn't relevant, when the redstone dust itself is not updating in a consistent, linear fashion. The underlying issue is that the code assumes what order things are updated in doesn't matter when they're all powered or unpowered on the same tick. However, there are various cases in which it certainly does matter, such as pistons, command blocks, and dispensers containing water buckets.

Is this still a concern in the latest Minecraft version 14w30c? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.

Is this still a concern in the current Minecraft version 1.8.1 Prerelease 3 / Launcher version 1.5.3 or later? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.

This issue should probably be marked as a feature request if Mojira supports that. The issue isn't a simple bug, but fixing it (assuming Mojang considers it broken) would require a significant rewrite to how redstone is calculated. I'm assuming it will be noted in a changelog if it ever does get fixed because as I say, it's not a simple undertaking. This behaviour has existed as long as redstone has, so I wouldn't be suprised if it's a "Won't Fix", but might be nice to get some word from Mojang if it's something they want to revisit.

Marking this as duplicate of MC-11193.
Feature requests aren't tracked on this site.