Probably that would be helpful for other eclipse rcp ramblers :). I have occasionally solved this problem. The way I was doing source file binding is probably broken for rcp dependencies and unless eclipse ide team fix it such way is unusable.
Good news there is much better solution - using source plugins (or osgi bundles what is the same). Once you have a source bundle you may add it to your target definition and enjoy source code navigation capabilities that eclipse ide provides.
However if you do not have source bundle, but have source code for some plugin you may create a source bundle. I dont know, if there is some tools for such task, I have managed creatinh my own source bundle taking an existing source bundle as an example and replacing plugin specific data with my own.