Ok, I think I may have a solution for you.
Try this:
Switch your eclipse workspace to the parent working folder of where your project folder exists (in your example, it would be c:\Source).
Make sure you don't have any pending changes on the files you wish to import. You can't do an import of files to a location where they already exist on disk so you'll need to delete them. So delete C:\Source\SomeProject (if there are by chance any files in there that aren't source controlled, be sure to copy them somewhere for the time being).
Now import SomeProject into this workspace. It should get the folder and its contents back to your working folder. This will add eclipse metadata to c:\Source, but its the best solution I have.
Everything under SomeProject will immediately show up renegade, but just do a get latest on that folder from the GUI client with the overwrite option selected to fix that. Unfortunately for now, switching between clients as you are, you will still have some trouble with the GUI client seeing files as renegade when they really aren't. I'm sorry about that, but we're looking into options to fix those issues.
Let me know if this solves your problem.
As for problems with Java 1.6.0_01, I haven't experienced any, but you are right that we aren't really recommending it yet. I will continue to look for problems with it.
Eclipse Plugin Problems (Check In, Pending Changes View)
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