When powering one face of a command block with a clock it has a chance to get stuck in the on position instead of pulsing. Removing the power source and connecting it to another face usually works.
Video explaining bug: https://www.youtube.com/watch?v=LneAPxUBCKo&feature=youtu.be
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You might want to double check your Description: "...will work with a comparator clock but not with a comparator clock...".

Thanks! I'm on a mac and I spelled conventional wrong then it automatically changed it to comparator.

OK after testing this I can confirm, however the description is not accurate.
This issue only occurs when powering the north face of a command block, the command is issued once then the command block stays powered, instead of toggling with each pulse.

I had this too so i connected it from another direction and it still only goes of once

Yeah some additional testing showed it to be inconsistent, ticket updated to reflect behavior.

I've got an even more interesting behavior! When I made a chain of command blocks and powered them with a comperator clock the first two just activated once, the others worked as intended.