OK, here's the problem and the solution. First, download this file - it will help illustrate the problem:
http://www.lostmarble.com/misc/Super-Boy-Problem.moho
This file has four copies of just the head portion of the character. Head #1 is the original head from Crazy Dan's file.
In Head #2, I selected all the points and smoothed them. It isn't really necessary to smooth them, but it shows us the problem. Between the top two points of the head (where the head and the hair join up), there are two connecting lines. When you try to fill the head or the hair, these lines appear to Moho as a double border. Even though the two curves seem to line up right on top of each other, the situation is almost exactly like the one Hiddicop illustrated earlier (his figure B).
To fix this, look at Head #3. On this copy of the head, I took the original head and deleted just one of the double connecting lines using the Delete Edge tool. If you delete both by accident, just add a new, single one back in using the Add Point tool. The hair and head are no longer ambiguous to Moho and can be filled.
Head #4 has the same structure as #3, but I went ahead and filled it to show it can be done.