Hmm. Well, after setting up favorites on my druid, I did not see those gems listed as favorites on my shaman. I don't remember being disconnected or otherwise logging out irregularly, but I suppose that's possible.
However, saving favorite gems globally is even worse... for 9 characters, I'll pretty much have EVERY WotLK gem listed as a favorite for some reason or another. I guess it's a few less levels of dropdowns to go through, at least.
Do you still have plans to implement gem mass-filling? I'd suggested it a year or so ago and you said you'd think about it. That would make things easier, if I could simply "fill all red sockets with Runed Scarlet Ruby".
Select the socketcolor, go to the gem you want to add to favourites for that socket and hold down CTRL and click the gem. (Just like it says on the tooltip when you mouse over a gem in the selection UI)
Layman version: You can't find an item in the list unless you have seen the item before (in your bags/equipped, on someone wearing it near you, or someone linking you the item (you have to click on it to download the tooltip)).
Geeky version: An item needs to be in your local cache before its tooltip is available to be scanned for stats.
You can try getting the itemlink from Wowhead. If it links successfully, the item has been seen by the server before. If it doesn't, the server hasn't seen it before since the last server reboot and you will just get plain text instead of a link. Repeatedly linking stuff the server hasn't seen before can get you disconnected.