When I let Web Compiler re-compile all files in my solution, it won't handle my compilerconfig.json files. Initially, I thought it was because they were leading with a BOM (Byte Order Mark), but I removed the BOMs, and the problem persists.
The output window shows this message: "Web Compiler found an error in compilerconfig.json".
Note that this only happens with the "re-compile all files in solution"-option (default shortcut: alt + shift + Y).