If this bug exists in JDK 5 then it is fairly fundamental and I would have expected developers the world over to have been yelling at Sun ( I don't think Oracle were on the scene for Java 5 ). I use inner classes though all my code and it all works well in Java 5 , 6 and 7.
It sounds to me like you have a bug in your build system. You could check the 'classes' directory ( or whatever you have called it ) after the compile step to see whether or not the class file has been created. If it has been created then you can check the jar file to see whether or not it contains the class file. In other words - check the build at each stage to make sure it is correct.