The UOP Changelog v1.5.0 (2006-10-07) mentions this: "Flawed ruby, emerald and diamond will now use the already created flawed icon and not the flawless icon also flawless topaz will now use the flawless icon and not the flawed one."
On UESP
https://en.uesp.net/wiki/Oblivion:Miscellaneous_Items in the Valuables section of the page it lists the changes the UOP makes to the gem icons. But either the UESP page is completely wrong or I think the icon changes should be reexamined. For the Diamond for example I think the flawed version should keep the flawed icon from vanilla and the normal version should instead use the new icon added by UOP. The same is true for the others I think.
And perhaps the icons for the Flawed Sapphire and Sapphire should be swapped? Since the Flawed one uses an icon which makes it seem more valuable that the standard icon.
Best to have a look yourself at the Valuables section and the entries plus pictures. I am not an expert on gems and I haven't checked them all in the game.