Did you try FontFinagler? I've seen a similar issue before with fonts displaying badly in one application but fine when copied into another - and usually the common ones too, like Arial and Helvetica. MacOSX caches fonts, and so do many applications, separately from the original files, and the caches can corrupt.
FontFinagler just clears all the caches so you get clean copies.
Emptying the Cache in Safari may help also.