Let me see if I can clear a couple of things up.
Linkster, FlashFXP does use the "CONNECT" method when connecting via a HTTP Proxy.
FlashFXP v2.1 has a bug that prevented SSL/TLS from working correctly with a HTTP Proxy. Other proxy types should be ok.
I don't know anything about ISA, what proxy types does it support?
You shouldn't have to restart FlashFXP for the proxy changes to take effect, you just need to reconnect to the site.
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