Well, I'd love to get this issue sorted out, but I really don't know where to start. I am reasonably sure my problem isn't a hardware issue since no other programs seem to be affected in any way, and my hard drives passed a thorough testing. Plus the problem never seems to affect more than one part per file, which is IMO much to consistant behavior for a hardware issue. Plus as I stated before, in emule when I forced it to accept the data, it checked out as good when the file completed. This wouldn't have happened if the problem was anything other than the program itself making the mistake. As to what the root of the mistake is, your guesss is as good as mine. The only thing I can think of, is if there are aware of any conflicts that may exist between bittorrent and protowall, since I started using protowall around the time the porblem started, that could be it. That could also explain why emule is having trouble too, since protowall is blocking packets at the driver level which is something a program may not typicall account for.
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