You could try setting the "Bind to IP" option in FlashFXP, this option can be set globally or per-site, depending on your network configuration this may or may not work.
Each network interface in windows has a priority and this priority is used to determine which interface is used by applications by default. When you use "Bind to IP" you ask windows use a specific interface, however in my experience windows doesn't always give you what you want, especially when either interface can be used to reach the destination.
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