There are some commands (in CM blocks) that fail to work consistently when there are multiple similer command blocks activated at the same time. The CM blocks that fail to work can be reset by simply changing the CM block type (ex: from reapeat to chain and back to reapeat), however this action will make other CM blocks around it stop working.

Steps to reproduce:
This bug can be replicated most easily with repeat command blocks set to always active. I was able to reproduce this bug by using rows of command blocks set with the command [execute @a ~~~ testforblock ~~-1~ quartz] and stepping on a quartz block.

Observed result:
Some of the CM blocks will fail to activate while others with the same command will activate.

Expected result:
All command blocks should still be working.

Note
I have tested this bug with multiple different commands and only a few of them produce this bug. It is most prominent with the testfor/testforblock command.