I didn't respond to your post because I really did not know the correct answer. Rather than give a half correct answer I waited for someone to post an in-depth response. Seems everyone was in doubt about the answer to your questions. All skills seemed to work fine for me, playing through without a second thought about the skills inner workings.

I looked at the skills and took a few screen shots. They seem to be a combination of percentages and points. The armor was the same way with a few percentages and points. The weapon skills I tried to max out the one or two I used the most without regard to "how much" they increased my weapons effectiveness. (see attached image)

I don't think an improper install would affect just the skills. I believe it would affect many aspects of the game in general.

The only problems with partial installs have been on Vista and Win7. I recommend the following for those systems.

If running Win 7 / Vista - Did you ...

Turn UAC off before installing.
Install as an administrator. (Right click the setup.exe, click "Run as an administrator")
Install in a directory outside of Program Files.
Right click the game shortcut, click Properties, click the Compatibility tab and check mark "Run this program as an administrator".
Try using different compatibility modes, starting with the newest and working back to the oldest?

DD likes the newest video drivers so make sure those are up to date.
Click here for ATI
Click here for Nvidia

If you did the above then the game should be fully installed and reading / writing to disk.
Hope this helps . . . =)

Edit: Found this - With skills, when you see that something adds x+y damage, that means it adds x to x+y damage. (For example, the first point of "augment damage" adds 1+2 damage. That means it adds 1-3 damage.)