Hi,
it looks strange. I've tried to reproduce it by following code and received a clean upload with no appended digits. Could you please try similar code on your place?
Sftp sftp = new Sftp();
try
{
    sftp.Connect("hostname");
    sftp.Login("username", "password");
    sftp.PutFile(@"c:\temp\file.txt", "MyRemoteFileName.txt");
    // list files on remote directory
    SftpItemCollection items = sftp.GetList();
    Console.WriteLine("Remote files:");
    foreach (SftpItem item in items)
    {
        Console.WriteLine(item.Name);                   
    }
}
finally
{
    sftp.Disconnect();
}
It produced following output:
Remote files:
MyRemoteFileName.txt
If the problem persists could you please create a communication log file as described at http://www.rebex.net/kb/logging.aspx and either edit your question to include the log or send it to support@rebex.net for analysis?