hoping there's an easy fix.
Sure there is. You need to pre-compose your line artwork and possibly your rotoscoped layer. This is a fundamental thing you need to understand about AE - the rendering pipeline and how "merging"/ "flattening" stuff via pre-compositions changes the internal order of operations and how specific tools and effects work just as well how it's useful to work with duplicates and use additional effects on top of existing done. You are simply using a bad workflow. Start by separating the roto process to its own comp and then re-use the resulting comp as a layer to be used as a matte on the line artwork, which also is it's own comp. Again, you need to structure your work better and understand some basic concepts. Indeed this is 100% user error by lack of knowledge. A short excursion to the help and some tutorials based on the keywords included in my hubub will do a lot for you...
Hi thanks a lot for getting back to me! So I've precomposed my line art work and am doing the same with the rotoscoped layer however this means I'm rotoscoping blind (what I was doing was painting in the roto layer, then referring back to the overall composition when I needed to be sure on detail where the line/figure met etc). By separating am I unable to view the progress of the rotoscope? Thanks