I think the blue ones are "new" as in, they were not in the popular section last week. They might have been last month or 2 weeks ago, but if they weren't last week, they get blue. I'm saying this comparing the rank of only 2 yellow and 2 blue ones, and although thsts what they indicate to be the coloring explanation, it's a fairly small number to be completely sure, so take this with a grain of doubt.
I waited a little over a week to test this theory. My results were that of the blue titles that I noted—waterside night, stigma, and in the dog house—all of them remained blue. The yellow ones stayed yellow, which would align with your theory. Maybe the titles are blue if they are "new" to the popular section for the first time?
Does anyone know why in the Popular Manga section some titles are blue and others are yellow?