I'm not obsessive about having neat backs, but I dislike having to stretch thread across wide areas if possible. So in a project that has polka dots, for example, if they are farther apart, I like anchoring my thread anew for each dot. Since I anchor by weaving my thread under, it doesn't work so well with just one stitch (a / leg and a \ leg only). So if the single stitch is surrounded by an already stitched area (again, like with polka dots), I usually weave the thread under a few surrounding stitches as well, which seems to hold okay.
So here's the problem with my current WIP. It's a Mill Hill kit on perforated paper, and it has several areas where there are single stitches off by themselves in the background. The problem is that with the large holes in the paper, you can see the thread jumping across wholes. Here's a closeup of the model to see what I mean:

You can see the yellow thread through the holes of the paper. So my question is, does anyone have any advice for how to anchor the stitches singly so that I don't have the yellow showing through the holes?