I had the same problem a few years back. Maya 2013... or maybe 2010. But i found the source of my problem. In my case, the curve was referenced. And when you attach motion path to the curve, maya will add locator shape object under the curve transform. Since the curve was referenced, i think it caused maya to crash whenever it tried to add the locator shapes during scene load. My solution was simply to delete the locator shapes and not using keyframe on the parameterU on that motion path. Instead I created an attribute and do the keyframe on that attribute. Then connect that attribute to the parameterU.
For flow path object, i suggest you group the objects under one transform and apply motion path on that group. Unless you want different motion on different object, maybe do it on duplicated curves.
That's all I can think of for now.