Provide screenshots including the layer palette or a sample file. It's unlikely that this has anything to do with color modes at all 'cos CAD and GIS programs usualyl don't care for that sort of thing and will export RGB coded colors in most cases. Therefore blaming them for something that they do anyway seem a bit far flung...
I can't provide screenshots of the actual project due to the sensitive nature. However, I have found exactly what I am having issues with:
If anyone has any advice or comments on this, please share it. I'm a new employee at this place and having to learn everything on my own and could use some help!
It is the use of transparency which causes all the layers below the on that is transparent to be rendered as an image. You will have to have the files re-exported from ARC with all transparency turned off.
I also use ArcMap to export layers out to Illustrator. The big problem I am finding is with fills in general. Some fills work, and some just confuse ArcMap into thinking it is an image (hence the bars of images, rather than vector lines)
If it is possible, have the person export the layers as "simple" objects (not cartographic, just lines with no fills) and that works like a charm for me. I do all of the styling in Illustrator anyway, so it doesn't matter what it looks like coming out of Arc. Good luck!