I'm having the same problem. Started a new project with Unity 5, Playmaker 1.7.8.3
I've noticed that changes to vars wont save, and that new actions added to states will disappear.
I've removed all plugins from the scene and the same thing continues.
Tried quitting Unity and restarting, and it seems that the first change will actually save but then subsequent ones wont. Once I tried readding an action a few times, each one disappeared after hitting play, then after restarting Unity, those actions appeared in the state, minus the existing actions. Really weird.
There are a couple warning/errors that appear in the Console:
"state.FSM != ActiveFsm
Unity Engine.Debug:LogError(Object)"
"Cleaning up leaked objects in scene since no game object, component or manager is referencing them PlayMakerGlobals has been leaked 1 times."
This is a tiny project at this stage so I could share if you need.
Cheers,
Jay