do you have osx? that would be easier for you to open a pdf and see how that highlight thing works.

I'll try to explain it again giving another example:

if you highlight a word, and then you highlight the entire sentence containing that world, with your script it will highlight the word with a different color, with osx it will display like you didn't highlight the word prior to this

your behavior only happens when two highlighted segments cross over, but none of them contain the other.