Hello,
When you connect from the local computer are you using the same site profile settings in FlashFXP? (i.e. FTP using Explicit SSL)
On the ISA FTP server do you have FTP SSL enabled and properly configured?
I attempted to reproduce this error on my Windows Server 2008 R2 but was unsuccessful.
This leads me to suspect that maybe there is something configured inbetween the remote client and server such as a transparent FTP monitor that is rejecting the "AUTH TLS" command (only allowing specifically defined commands)
A google search lead me to the following webpage which appears to report an identical problem as well as the solution
Part 1: Publishing IIS7 secure FTPS with TLS aut via ISA => 550 access IS Denied - Tom Decaluwé