If you assign your bonus points and do not press the check mark button, the assignment will be lost. You still have the points and they can be reassigned just be sure to press the check mark button afterward. What happens usually is someone assigns the points and then presses the red skills update arrow to update the skills without pressing the check mark causing the assignment to fail. See attached image.
When referring to the setup.exe we are really referring to the setup_divine_divinity.exe. We are just lazy and don't want to type it all out . . . =)
You would install as an administrator by right clicking the setup_divine_divinity.exe file and left clicking "Run as an administrator" on the resulting dialog.

OK, thanks. But my bonus points really are gone for good.
I'm trying re-downloading and saving the download, instead of running.
Then running the .exe file as an admin. Hopefully, that works?

Yeah, you really need to download the entire setup file before trying to install. After downloading, run the setup as an admin as described above. After installing, right click the game shortcut and make sure you check mark "Run this program as an administrator". Using a compatibility mode is dependent on each system so use one that works best for you or none at all if that works. . . . =)
Edit: You might want to turn UAC off before installing and turn it on afterward. The setup.exe is 1.6 GB's so it may take a while to download depending on your speed.

Always save the copy - that way you've got a backup if you need to reinstall.
Would also recommend youdon't install the game into Program Files - use a custom folder

Also, not sure how you installed the first time, you should backup any saves you have and uninstall the existing install before reinstalling the game.
After uninstalling, delete any Divine Divinity directories / files under C:\Program Files\GoG.com\Divnine Divinity before reinstalling as well.
As Kezrdin suggested, installing in a directory outside of Program Files is a good idea. I create one name Games on C drive. After right clicking the setup.exe and clicking "Run as an administrator", on the first GOG installer dialog, press the options button in the lower left corner and direct the install to the new directory.

The above tips worked....
Thanks, folks!

That's great ! It's a fun game, enjoy . . . =)