The source lookup will be showing you source code from eclipse, but what is actually being executed will be what is on the server. It is possible that the two don't match up.
You may be tracing through it (step by step) and looking at source code, but the server is executing different code. Sometimes eclipse can recognize a mismatch between what code you're browsing and what is actually being executed, but it will not be able to show you the code from the server.
Hope this helps.