There's an alternative to highlighting scanned copies of PDF. Go to customized settings tool, under Comments section, you'll see drawing markups. Add the LINE to your quick tools and you can use this to give the highlighting effect. You can change the properties of line, by right click on the line and changing the color, thickness and make it default. Works for me.
I'm using Acrobat X, but I assume the concept is the same for all versions.
Hope this helps