WebSite Onpage Analye regards those words which have less 3 chars as stop words by default.
this problem is easy to reproduce:
1. first go to (Preferences -> Edit stopwords) empty the stop words.
2. anlyer any web page that have words with less 3 chars, And you can not see any words with 1 or chars in the keywords cloundmaps.
for example:
do onpage analye on webpage http://www.link-assistant.com/seo-softw ... uages.html
you'll not see any of these words(a, is, in, to .. etc) in keywords cloundmaps .

I did that for three keywords - "in", "at", "a".

As you can see from the screenshots below - they are take into account - they are highlighted, density is measured etc.

here i the keywords must have more than 2 chars not mean the keywords in "enter your keywords to opimizer your page" step.

for example: i'll opimize keywords "seo software" for a page only contain "is", "of", "in", "a", "an", "or" etc simple words, such words will not appear in the page elements's keywords list( or keywords cloundmaps), they were regard as stop keywords by default, but the keywords you entered in the step 2: "enter your keywords to opimizer your page" were there.

asume a page conains only one char (or two chars) keywords, and when page were anlyzed, in the page element's keywords list, only the keywords you inputed in step 2 were there. nothing else. just like we have anlyzed an empty page.

i use an page body contain


input "is software"


anlyzed keywords list, lost "a", "an", etc 2 char words, only "is" appears (which inputed in step 2).