So, I've narrowed down the problem.
Forgot to mention that we're using PlayMaker 1.8.9 on Unity 2018.1.0f2.
We have some fsm templates which expose some "inspector" variables, these templates are then used in Run FSM actions by other fsms.
One of the designers removed some of the inspector variables from some of the templates and now wherever they are used we're having this null reference exception.
Looking at the YAML for the assets I can see that the removed variables are still referenced in there, thus causing the error.
A fix to this is to just disable/enable the affected Run FSM actions, but we have more than 600 instances of those throughout the project!!
Any ideas?
Thanks!