The crux of the matter is that people have figured out how to manipulate the pricing stats. If you search for one of these gems, the interface will typically tell you something like the following:
Price per Unit: 13,327
Average Last 10: 6,457
People will put up these gems at 100 gold and then immediately buy them back themselves just to drive down the Average Last 10 number.
The effect on a player who just wants to sell gems: the game will auto complete the sell price at 6,457 for them. These players get tricked by the game mechanics into grossly underpricing their gems.
The effect on a player who wishes to buy gems for craft: they are forced to put up purchase orders for the gem at a ridiculous price, 13,327. You have to essentially gamble on someone underpricing a gem, or gamble on catching one of the manipulators selling a gem for 100 gold. Most of the time you will end up buying the gem at a loss.
If game didn't allow you to buy back your own gems, then this might fix the issue. A manipulator would be guaranteed to give away his 100g gem at a huge loss, and overall the prices presented via the AH UI would more or less accurately portray the current cost of the gem.
As it stands, the experience of trying to ply the gem trade on the AH is extremely disappointing.