You may still have the folder created by the self-extracting zip during the beginning of the v2 install. When the updater ran, did it say it was a v3 or a v2 updater?
If you still have the old folder, when the updater.exe is run, a self-extracting zip creates a folder called "FMP_Updater". When v3 is installed, the self-extracting zip uses the same folder as v2, but does not overwrite the files within it. Once the files are extracted, the v2 updater kicks off instead of v3.
Solution: Rename, delete, or move the original "FMP_Updater" folder.
Please let me know if this works for you.
TS_Oz, FileMaker Inc.
Thanks for your help.
You were right, the old folder was still in place. Removed and fixed problem.