Having FlashFXP Window resized:
http://imgur.com/hVV9i.jpg
Maximizing it:
http://imgur.com/xQc5r.jpg
After minimize and restore from tray:
http://imgur.com/5MavI.jpg
(Sorry for all the blurring in the images)
It seems after further testing, the progress bar at times goes back to the right position, depending on the size of the window when FlashFXP is not maximized.
It's not really a big deal, so don't waste too much time on it