When using the new Jucer under Windows (7/64 bit, git tip is from somewhere last week) the additional includes path for JuceLibraryCode is “…\JuceLibraryCode\AppConfig.h”. The reason for this should be that the path is generated with RelativePath::getParentDirectory() which looks for the last occurrance of “/”. Since Windows uses the backslash (maybe not always in the API but on the systems I tried) it can’t find a last slash and leaves the AppConfig.h appended.
Also the documentation for upToLastOccurrence() and upToFirstOccurrence might be mixed up. In the above mentioned getParentDirectory() upToLastOccurrance() returns the full string without having found the substring, but the documentation says it should return an empty string.
Edit: Changed subject to make a bit more sense.