1. This is the normal behavior, FlashFXP will use the SIZE or MLST command to determine if the file exists before uploading. You can disable this feature by unchecking the option "Request file size/date prior to transfer" in the File Transfer Rules dialog, however by doing this you will reduce accuracy of the file transfer rules and increase the likelihood of the wrong rule being used.
2. At the moment the update check cannot be turned off, we will be allowing users to disable it in a future release.
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