I think the same thing happened to me. (I'm also new to SVN and use Cornerstone). I did a removal from Cornerstone instead of Finder and it seems to work very well, with no missing icon. I get a red D icon, then I commit and there is no ghost file or is missing! icon.
I just tried deleting a working copy from the directory and what! the icon and the ghost file are missing, but if I right-click on the ghost file and select delete, I get the D icon. Then Commit, everything is fine ... there is no more ghost file.
I am updating my version of Cornerstone. I'm on v2.5.2. Maybe something that was fixed in Cornerston? I think I remember that I had the same experience as you by 1 point. I think I left Cornerstone, opened it, selected this working copy, and then clicked Update, and he fixed it, but not sure though ...
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