that's interesting. i noticed something else odd. if you choose to unlearn a skill, and pay the fee, but then cancel the skill screen, you still get charged the fee. i noticed this when i was examining what i wanted to do, and was trying to figure out which skill i wanted to drop. changing my mind i cancelled and then did it again. having 50,000 gold, i had none but only really unlearned 2 skills at 10,000 gold each. i cancelled 3 times before deciding to go with 2 different skills. i never had an issue with the skill points as you describe, but after cancelling 3 times, unbeknownst to me, i had 20,000 left so when i decided which skills i wanted to drop, i did, and had no gold left.
