If you update a world made in 15w34d with some Conditional Command Blocks in it to a higher version (15w35a or higher), the game forgets which command blocks were conditional and wich were not.
Instead all command blocks are treated as unconditional.

As I built a rather large contraption it is very painful to "re-condition" all of the command_blocks.

Maybe there is a way to fix this issue, maybe there isn't.