I know this thread is a couple years old, but I just stumbled on it because I was having the same problem.
I'm partially colorblind so I couldn't tell when Inventor was highlighting something that I selected (ie dark blue and blue look the same to me. go figure). I didn't realize that I just wasn't seeing it until a coworker told me that it was definitely changing colors.
Changing my color theme to high contrast fixed this problem for me. I hate the color scheme and wish that I could select what colors represent what, but at least I can see what's going on now (I'd really like to have the scheme do red for under defined, blue for fully defined, white for mouse-over, and green for highlighting; would it really be so difficult to allow users to input the colors they want?).
To change your color settings go to the "Tools" part of the ribbon, click "Application Options", click the "Colors" tab and select the color scheme that you like best.
For ease of reading:
Tools > Application Options > Colors > Color Scheme
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