in v3.6 when you do "copy url" you copy the ftp:// url so that other people with ftp clients can quickly login to the site simply by clicking the link.
in 4.0 RC2 there are several different copy to clipboard options, including a copy http url.
You might want to try
FlashFXP v4.0 RC2, I believe it might correct the 24 hour time format issue you are experiencing as well.