FlashFXP 2.1 runs semi somewhat ok under Wine.
But there is bugs, I submitted the most crusial to WineHQ, they havent bothered to answer.
http://bugs.winehq.org/show_bug.cgi?id=2328
Using the 20040408 wine version keeps your settings, sites, and stats.
To list the other bugs briefly:
You cant double click with your mouse to change dirs, just use the keyboard
You cant use the site manager
You cant read some of the text in the prefs menu
No tray support to hide FFXP
No queue info
There is some other bugs too that i found, but I dont remember them atm.
Using WineX3.3.x solves some of these issues, but running FlashFXP under WineX breaks the SSL features.