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This is an old problem related to the unwillingness to read the manuals ;) The solution is simple - during the turn of the dwarven unit, pay attention to the Action Points (AP) bar - the runes that the unit can activate will be displayed above it (and the player decides whether this activation is needed).
That's the problem... when I hover over a rune, it says "Used" and the amount of resources on the right, but nothing happens when I click... that is, I can't use it...
Here's how it looks in the screenshot...

Added 8 minutes later
and also... I'm using a noCD for the game... could this be a problem? If so, where can I download a good noCD, or will only a disk image work?