My ISA is setup very similarly to your own,
Are your clients using the ISA firewall client ????
My clients use it and i have no problems using flashFXP on them
If you dont use it try it, you dont need to enter any details into any applications such as proxies etc, its as if the client is directly connected to the internet
Software is located at :
\\ISASERVER\mspclnt
its installed by default on the ISA server,
You can edit the firewall client details using the ISA MMC
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