We found a problem with Negotiate Date CF and Pause SLA. It seems that coming back to from pause stops a clock.
In our scenario we have several clocks for given workflow and one of them is based on Negotiate Date CF. It has JQL trigger that enables it when Negotiate Date IS NOT EMPTY (all others clocks has counter-condition Negotiate Date IS EMPTY). Basically that work very well until Pause status is activated.
Let me know if you need more details! Thanks Łukasz K.