It works as it is designed to work. Enabling CR changes the internal rendering order. Write-On is just a pixel-based effect, anyway, so you achieve nothing. Either you start over using much larger layers, rebuild it e.g. using shape layers or you simply leave it as it is.
I'm glad it works as it's meant to work. I'll be sure to write to Adobe and congratulate them.
Not looking over your shoulder and not knowing your comfort level with AE, I'd probably approach this by precomping the vector layers under the write on effect or even prerendering that layer and bringing it back in as a movie that just gets revealed with the write on masking.
Continuous raster is a weird function because of where it appears in the render lineup or pipeline. After all these years, I just push the button and wonder what will happen. I'm usually surprised that my expectations were incorrect.