I was attempting to use FontForge to combine the light and regular versions of the Muli font (OFL licensed sans serif) into a semi-light font, and found that FontForge produced a completely unusable result, with some glyphs distorted to the point that they were unrecognizable as letters/numbers. By contrast, Fontographer had no difficulty creating a great-looking merged copy of that font. This seems like a part of FontForge that could stand some enhancement.
I would try doing a ‘canonical contours’ and ‘canonical start point’ before doing the interpolation. They are under Element->Simplify