I wouldn't say Varric actually disliked Seb. More just didn't really 'get' him. I mean, Varric is a storyteller, he's used to the fact that every single person of importance has their good sides and their bad. It's part of what makes the great heroes, like Hawke, fascinating enough for him to make up the bullshit stories Cassandra loves so much.
But with Sebastian, Varric runs into a man who is so absolutely genuine, it throws him for a loop. Varric just doesn't understand how a person like Sebastian can exist. He's got to have some kind of angle, some sort of secret or private agenda, some flaw the creeps up now and again to bring Sebastian's dreams crashing down in a spectacular tragic ending. That's the world that Varric knows and expects. Sebastian's deadpan sense of humor doesn't help Varric's opinion of him. Their relationship begins with Varric thinking he's incapable of humor.
Over time, Varric gets to know Sebastian and the flaws the man has. But at first glance there doesn't appear to be much to work with. Varric could make an interesting and fascinating story about Sebastian. The problem is that there's not too much room for bullshit. That's not something that Varric is used to. So he spends half his time with Sebastian shaking his head in disbelief. The later later banter between them shows that the reach something of an understanding with one another.
- Sebastian: Your Merchants Guild reminds me of the court at Starkhaven. Intrigue and gossip wrapped in a layer of formality.
- Varric: If Starkhaven was a tenth as bad, I see why you took to the Chantry.
- Sebastian: Fashion was the worst part. In the Chantry, I never have to worry whether doublets are meant to be fitted or padded this year.
- Varric: In Starkhaven, do they bludgeon you to death for forgetting the name of a minor clerk's third daughter?
- Sebastian: Only if you're lucky.
- Varric: Choir Boy, suddenly your life makes much more sense to me.