How to recreate:
Have a repeating command block set to something like /particle. Switch it to Always Active and you should see the particle.
Make another repeating command block with a /clone command and turn it on.
The other command block will turn off, and won't reactive unti lyou update the command. (not a block update)
I'm unable to reproduce this; I've got one command block running in parallel to the particle command block, and both are executing properly.