I was able to repro this and it looks like this is not working as I intended. If an item has only 3 enchantments or less, you should still be able to use a gem to add to any one of them, up to the player-created maximum of +3 for things like saves, skill, ability, enhancement, or AC bonuses.
I'll work to get this changed by the server update this weekend.
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EDIT: Well, scratch that. I spent a couple hours looking at this and now I remember why this is as it is - it would require some major rewrites of the enchantment forge code to allow someone to further enchant an item that already has 3 enchantments on it. So, unfortunately, this is the way it is going to stay. I'd suggest everyone get those first two enchantments on an item just the way you want them, and only after that, add the third - at which point the item is 'locked' as far as magical enchantments go, and cannot be modified further (except to remove enchantments, if you wish).
I'll keep this on my wishlist of things to change, but right now it is not a priority.
I'll work to get this changed by the server update this weekend.
----------------------------
EDIT: Well, scratch that. I spent a couple hours looking at this and now I remember why this is as it is - it would require some major rewrites of the enchantment forge code to allow someone to further enchant an item that already has 3 enchantments on it. So, unfortunately, this is the way it is going to stay. I'd suggest everyone get those first two enchantments on an item just the way you want them, and only after that, add the third - at which point the item is 'locked' as far as magical enchantments go, and cannot be modified further (except to remove enchantments, if you wish).
I'll keep this on my wishlist of things to change, but right now it is not a priority.