What version of Rstudio are you using? Also, what operating system. I created a vignette for a package on my mac over the weekend, I use the dark theme but I remember it being very readable.
Also, I was wondering if you see a difference viewing the vignette in the viewer, or in it's own window?
I'm on RStudio version 1.1.383 running on a Windows 7 desktop. And yes, I see a difference viewing the vignette in the Help viewer vs. its own window. In the latter, the background color renders properly, in the Help viewer it defaults to the background theme color. A plain vanilla test package can be downloaded from here (this is the default devtools package + default vignette + custom CSS file). The background vignette color should be a dull yellow.