IIS may redirect directories/folders. FileZilla Server and the clients are not aware of this so the following situation may occur:
1. IIS creates empty directories on the HDD.
2. The directories are then redirected to the IIS structure. So the physical directories stay empty all the time, they only serve as placeholders.
3. FileZilla isn't aware of this and writes the files into the real directories (as it isn't integrated into Windows). Because of the redirection you won't see them there, but as they have been transferred successfully, there's no error.
I that assumption is true, there's unfortunately no real solution. If it's only an account problem (FZ Server runs under SYSTEM, which may be excluded from redirection), then it may help to include that account or run FZ Server under a different one.
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FTP connection problems? Do yourself a favor and read Network Configuration
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