From what I can tell, it's something to do with the Level 25 Trade skill perks of both Appraiser and Whole Seller. It doesn't matter which ones you choose but this is the way I BELIEVE it's supposed to work:
Without either of the skills, you CANNOT see the above or below average price indicators of the green/red of the price.
Without either of the skills, you are SUPPOSED to see the green and red of stat differences between two items.
With either of the skills, you are SUPPOSED to see the above or below average price indicators of the green/red of the price.
With either of the skills, you are SUPPOSED to see the green and red of stat differences between two items.
How I believe it currently works is:
Without either of the skills, you CAN see the above or below average price indicators of the green/red of the price.
Without either of the skills, you CAN see the green and red of stat differences between two items.
With either of the skills, you CAN see the above or below average price indicators of the green/red of the price.
With either of the skills, you CANNOT see the green and red of stat differences between two items.
For now, I have been skipping the Level 25 tier of Trade perks entirely and have not lost the ability to see both above/below average price marks NOR stat up/downgrades when comparing items.