I have found that when I need to rename a Java class (and therefore the source file) or need to change the package name (and therefore move the source file[s]), I can either
I hate to walk in and say 'ur doin it rong', but since your subject line mention Subclipse - Subclipse integrates with Eclipse's refactoring tools. So does Subversive. When you rename a class, it executes the 'svn mv' for you underneath. You should never need to attempt to replicate those moves manually.
I wonder if for some reason Subclipse is not attaching to your project - if it doesn't know your project's a Subversion project. Then obviously it wouldn't do anything.
If you're not using Subclipse/Subversive... start. :)