I totally agree, You shouldn't have to fix anything, but this day an age with so many different software programs on the market there are bound to be conflicts and issues. Not every program is perfect. We try to make every users experience a great experience, I'll be happy to work with you in any way I can to help resolve this problem. I would love to see these long standing issues with ZA resolved.
I have to ask though, Did you try the winsock fix? If you didn't can you please try it and see if it makes any difference. You may have to reboot after applying the fix, I'm not entirely sure.
The FlashFXP IE plugin is only for downloading, It installs a BHO which detects when you click on a
ftp:// url in IE.
The winsock fix will not fix anything directly related to FlashFXP, Since FlashFXP doesn't install any low level winsock helpers. However ZA does, I believe even windows firewall does and maybe switching from windows firewall to ZA causes this problem one some systems.
Take a look at this page I found via google
http://www.testmy.net/topic-2821.msg27437;topicseen
The last post states that after running the winsock xp fix the user was able to upload.
If this does fix your problem perhaps ZA should have a built in method that performs the exact same fix if needed. That way ZA users wont have to deal with this problem.
I totally agree that anti-virus or firewall software should never be permanently disabled, disabling it temporally to determine if there is a conflict may be needed from time to time. Some applications actually ask you to disable anti-virus software during installation, I don't agree with this but in some cases it's a necessary evil.