Do you happen to know exactly what version/build of FlashFXP you upgraded from?
We've had several customers report this issue but we are unable to reproduce this behavior or determine exactly what is causing it.
This is quite a mystery to me and it's quite odd that it would comes up now, We've been using this new installer system for nearly a year without any issues.
Removing FlashFXP and re-installing it seems to resolve the issue, As you noticed, and all FlashFXP settings and sites are preserved provided you don't choose to remove them as part of the uninstallation process.
As MxxCon pointed out FlashFXP runs under wine on most Linux distros; for the best experience we recommend using the latest FlashFXP v5.x beta releases.
http://www.flashfxp.com/forum/flashf...x-public-beta/