The red outline polygons usually indicate polygons that won't triangulate, perhaps because there are duplicate vertices at the same position, or edges are crossing. Try selecting one of the surfaces and switchcing to vertex mode to see (at the top of the controlpanel) how many vertices you have in that surface. If you have > 3, that's the problem.
You could also try selecting the red surfaces and try combining them (surface->combine).
If that doesn't work, you can try deleting them then creatinga new surface between the vertices.
If all else fails, send me the file and I'll have a look at it.
Andy
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