Fonts include hints (there are different types on hints, and different formats of fonts, and some tools that can break or do not support them) as to how they should be placed in relation to other characters, rather than the bounds of the characters themselves which can look somewhat ugly (think monospace). If the container is accidently using these hints to work out wrapping or justification spaces, you will run into situations where parts of the character go over the edge.
FontForge is a very powerful tool for working with fonts, it requires you experiment a little bit - but you should be able to find the options for rebuilding a lot of the data which might be missing or incorrect. It however is not intended to be run on Windows. Mingw/cygwin are two different ways to get Linux code working on Windows.
The new build uses cygwin, just extract the file and run the bat file, it will extract and run the tool.