Have same issues long time ago)
Only Conclusion I find – not load res in project A from other place then project A 
For all others res use external folder “…/…/res” links good same in eclipse and after project was built.
p.s personaly i now using abs Path - easy to debug
String workingDir = System.getProperty("user.dir");
String IO_Path_ABS = workingDir + "\\";
File file = new File(IO_Path_ABS + str);
but long time ago i use this)
protected File get_File_In_Jar_In(String path){
URL ur = SomeClass.class.getClassLoader().getResource(path);
File file = null;
try{
file = new File(ur.toURI());
}catch (URISyntaxException e){e.printStackTrace();}
return file;
}
protected File get_File_In_Folder_In(String path){
File file = new File(path);
return file;
}