The theme score in WCS is calculated using a number of different factors, including:

• The number of theme words and phrases you have in your article.
• The number of theme words you have selected.
• The length of the article.

The software looks to see if you have used all of the theme words you specified in your list.  If you have, then you'll likely achieve a good theme score.  However, the Quality theme score is there to stop you over-optimizing your article.  It uses those factors mentioned above, but also looks more specifically at the use of the theme words and may award penalties for your article if:

• The density of theme words in the article is too high.
• Certain theme words or phrases are used too many times.
• You are not including enough of your chosen theme words.

The first two things are determined in the settings of WCS.  I have a default set that I use and update periodically.  You can load those on the settings screen if you have changed anything.