Hmmm... I downloaded the latest and greatest Saab_340A_1.5.zip (containing a S340A-windows-installer.exe dated 2018-03-16 22:08) this morning and ran the installer. It stated that it was uninstalling the previous version, then installed the new one... Really followed the instructions "to the letter" AFAIK/can remember... I can certainly redo it and explicitely uninstall the previous/now current, version before running the installer...
10 minutes later - Cleaned out the old version "by hand", also removing the old GizmoLog.txt. Reran the same installer. Now, as you say, the problem is gone and "all is fine" - I do see the two "LES: Load Saab 340A..." lines in the log.
But, that does give a possibility that the general upgrade path isn't always working as expected... But, since my initial installation was (partly?) removed by my first try, it's hard to regenerate the behaviour...
One observation though - With the latest installation I'm unable to get the Gizmo Console to show... There is a GizmoLog.txt file and it says "Called: Console_OnShow", but nothing visible happens when I trigger the Console (top button on the right edge Gizmo menu). The other entries work, but the console is gone...