Yeah, I tried looking at it on both Opera and Chrome (I primarily use Opera), in case it was a browser thing, but it looks exactly the same in both browsers, so that's what made me think there might be more to change.

I tried using all percentages to modify primary/secondary and the navlinks, but 85% + 15% leaves a lot of empty space in between the sidebar and entries which just seems really weird.

I used the following CSS for what my journal looks like now:
.two-columns-right #primary {width: 93%;}

.two-columns-right #secondary {width: 21em;}

.two-columns-right .module-navlinks {right:21em;}

and I like the way that looks. Would it still be a good idea to submit a support request, then, and mention the percentage/ems mixup thing? Even though I have the journal looking the way I like it, I mean.