Let me document one of the fixes here (that way when someone Googles the same problem they might find the solution). Part of the work of "ChkTeX for TeXShop" is handled by an application that uses the Web Page display capabilities of Platypus 4.0 <http://www.sveinbjorn.org/platypus>. Now, the two considerations to make here are:
1. The meta tag must be: <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /> 2. The output should be piped through iconv: | iconv -f UTF-8 -t LATIN1 --unicode-subst="%u;"
Both of these fixes are because the web page has to be iso-8859-1 encoded.