@BigStar, thanks for the recommendation. I will set it to Binary Mode.
One thing I noticed by carefully looking for the filter settings in FileZilla, that they don't include PHP files for ASCII mode by default. Perhaps this is the reason why there isn't a problem with that client app.
One more question to you BigStar?
When I set FlashFXP to download in Binary, in Notepad++ it displays the formatting of the file to be Windows/DOS, where the original file was formatted for UNIX. Is there a way to also fix that? Or is that still normal?
I don't know what kind of settings MS FrontPage has on it's built-in FTP, but when I use that to backup my site, the files are all perfect UNIX / without space lines in between.
Also, I found this explanation about Pure-FTPd, which my server seems to run (according to the info provided in the above Session Logs). May be something you guys can read?
http://www.novell.com/support/kb/doc.php?id=7008378
Threaded Mode