Well strike me down with a feather....
That time it worked.
Previously I had tried to download the ispconfig-126.96.36.199.tar.gz and then run the update script, that's when I had the problem with the database already containing tables....
This time I used the Manual Update instructions and downloaded ISPConfig-3-stable.tar.gz. Running the script after unpacking worked a treat and actually updated to ISPConfig-188.8.131.52.
Would still love to have a HowTo manual for ISPConfig 3.x