Rune Central

Zopmod is an old mod that does allow holding two runes, but it's not based off of Rune Quake insomuch as dual runes.

The 'tinking' issue is due to a rune being stuck in a wall, and hitting insides of the wall repeatedly. Typically, the rune will travel away, and the sound fades out, or it will come out of the wall. I have seen it where s rune doesn't seem to be moving, and incessantly make sound, but it really is moving; otherwise, no sound would play. At least, that is what I expect with an entity with MOVETYTPE_BOUNCE.

I think a touch counter (such as 20 world touches before the rune is moved) would be more effective in detecting rogue runes.

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a random mod server: zop.runequake.com

I'm too lazy to test, but I did look in the server source code to see what FL_ITEM does. It automatically adds 15 units to every side of the item's borders. Removing the flag doesn't sound like a fix- runes would still get into walls, especially if smaller... probably?

I think your idea of using a bigger size entity to check spawn location is on the right track. One theory is that the issue could be caused by runes' spawnpoints. These could be anything, other than a few rules (See SelectSpawnPoint). So a torch's location on the wall might cause a rune to spawn partway in the wall (and the random velocity could be pointed into the wall). This could happen similarly with items on the floor and so on.

Another option might be deleting a rune if it touches world within 0.5 seconds or somesuch after spawning... but this idea is only valid if my theory is correct. On the other hand, I've seen runes fall into the ground without sound... I'm much too lazy to test... the tinking sound might happen once a level.

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a random mod server: zop.runequake.com