Hi Philo, the problem is that the 'head' model is nearly coincident (ie locally co-planar) with the hair model in lots of places. This is a problem for the current meshmixer booleans implementation (I have some ways to improve it, but ultimately all boolean implementations have problems with coincident areas). Remeshing won't really help here, unless you remesh to a level that is small enough that the boundaries of the coincident areas can be resolved (which could be really high in this case).
One way to fix it is to scale up the head a little bit. But possibly this is not a reasonable solution for you.
Another is to use the D1 mode of VolumeBrush to "fill in" the hair interior surface, as in the image I have attached. If you do this in the right places the surfaces will be separated and the difference will work. It seems like the problem area is where the cylinder meets the hair around the rim at the front (under bangs etc).
To get a better view of what is going on you can select all that interior junk, and smooth it like crazy using the smooth tool. To get the selection you need to paint as much as you can and then right-click-and-drag to expand the selection, so it gets the hidden areas (this will pause for a second or two). Then run the Smooth tool and bang on the right-arrow key until things stop changing. See second set of attached images.