I have a similar problem, I tried the solution changing to ACTIVE mode and the files are uploading now still some files are not uploaded and it still takes a long time to upload each file and the size of each is only a few kb! I'm pulling my hard trying to upload only 7MB the last 2 days.
I hit allow flashfxp when the window firewall asked, what else should be done?
I tried on 3 different pcs window8 and window 8.1 and all got the same problem.
Update: I borrowed my uncle his machine is window 7 with flashfxp 4.4.1 and had no problem uploading whatsoever.
So it seems the issue is with flashfxp latest version and window 8?
Btw, I have AVG anti virus installed on my window 8.1 machine.
Firewall I just use the default that came with window
Please see the zip file for 2 logs: one is with active mode and one is passive mode by default
Threaded Mode