Two sites [L] and [R]
When FXP'ing securely using SSCN from [L] to [R], FlashFXP will by default, set the [R] side to SSL Client Mode handshake using SSCN ON. If you then securely FXP (within the same two ftp sessions) in the opposite direction, from [R] to [L], FlashFXP will set the SSL Client mode on the [L] side. This leaves both sides in SSL Client mode and the handshake for the transfer fails.
The way I read the spec, SSCN is set for an entire session unless it is changed otherwise.
This is the best spec I can find --
http://www.raidenftpd.com/kb/kb000000037.htm
This is the current build -- 3.4 ? (I just updated to see if it was fixed)