Hm, I suspect there is something else causing you trouble than the files on the server. I just did a complete patch starting with no files and got everything.
Debugging info may be the only thing that'd help at this point. Are you using .NET Framework 1.1 or the 2.0 beta?
I'll do some brainstorming and see if any other things that could be causing this cross my mind.
Quib
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