I'm using jFTP v5 and there is nothing in POPUPLOG.OS2 - it worked without problems before the update
I am using jFTP v5.01 (presumably from the same place that you got v5). I have seen no problems with it. I use this, in jftp.cmd, to start it:
java -Xmx512m -Xms32m -jar jftp-5.0.1.jar
FWIW, I use jFTP to download test versions of ArcaOS, and they are near 1 GB in size. You may have problems, if something is using too much lower shared memory space.
Since you mention security updates for Samba I assume they carry over to other network programs than can use them so I will start looking there
No. SAMBA does it's own security. Other programs do to, but I don't think there was anything added to them.
Is there a list of these security updates anywhere and what one has to do to reset them for SMB client?
Have you read the PDF and README files, in the root of the DVD? You can mount the DVD ISO as a drive, by double clicking the ISO (change the default drive letter, if you wish), and click MOUNT. Eject the ISO by using the REMM widget (REmovable Media Manager - the same thing that you use to eject USB sticks), when you are finished.