Disclaimer: I don't own anything from Merlin, although an Arthur to call my own would be nice.
Uther was suspicious of the boy from the start.
When the witch threw the knife, the boy seemed to move a little too fast; but Uther shook it off as his imagination.
Then there was the business with the snakes suddenly appearing from the shield, and the time where his son, his ward and the boy disappeared; and when they returned the mysterious illness had disappeared.
Uther dismissed these, along with what happened with the Griffin and numerous other incidents, having no proof.
But then, during the fiasco with Tristan rising from the dead, Uther got the proof he needed.
He wasn't as ignorant of magic as people thought; he remembered many things he had been taught when he was but a child.
And so, when the boy appeared with a sword that could slay the dead, Uther knew he had a sorcerer in his household.
But... Uther had also seen the changes in his son since the boy had arrived; had seen Arthur becoming a better man.
His son had even begun challenging his orders, following his own morals; something Uther had been hoping for, and trying to provoke, for many years.
So Uther kept silent, watching the boy silently as he worked (and deflated his son's ego), waiting for any sign of trouble.
He didn't think the boy was evil, especially after the events surrounding Arthur's bite from the Questing Beast.
Uther knew the price of giving life, and was surprised (and slightly afraid) when the boy returned with Gaius, soaking wet and injured but very much alive.
So Uther resolved to wait until the magic finally corrupted the boy: Merlin.
So, I was watching the first series of Merlin back-to-back today and, while watching Excalibur I thought Uther must have been a bit suspicious. After all Pellinore's sword went right through the zombie without hurting it at all, in pretty much the same place, and yet it bursts into flames when Excalibur touches it. And Uther can't be that stupid; he must have had some education in magic while he was growing up. So this was born.
Please read & review; they make up for the bucket load of work I have to do at the moment.