Okay, this problem didn't surface in the previous snapshot because conditional command blocks were completely broken. Anyway, the issue is that the SuccessCount tags on conditional command blocks are simply not being updated. This causes the following issues: If you have a chain of conditional command blocks following a repeating command block (always active) done in this manner:

/testfor @a[r=3]

/say hello

/say hello

What happens is that the chat will spam with "hello" from both first and second conditional chain command blocks when a player is within 3 blocks of the repeating command block. When the player exceeds the 3 block range, the second conditional chain command block will continue to execute the command. This hence defeats the purpose of having a chain of conditional command blocks.