You can create new files logged in as the same user, but are you trying to do exactly what the app is trying to do Is it creating new files or editing existing ones
.NET's file access is just a wrapper around the underlying Win32 file APIs. The only extra security it adds is code access security, and it sounds like you're on top of that.
The first thing I'd try is to see if it's something more specific like a problem with ACLs on a particular file or directory - just because you can create new files in the share doesn't mean writes will work anywhere in that share.
Also, try writing a very simple test app that just creates the same files with the same names and in the same places as you tried via Explorer.
If you still find that the behaviour from your .NET code is different, then we'll go from there, but my suspicion is that it's probably not a difference between .NET file access and normal file access - I think it's more likely to be something specific to what you're trying to do with the file.
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