Bunny behavior- Neutered male dwarf showing signs of aggression

Question
I got my dwarf rabbit from a breeder when he was 3 months old. The breeder recommended getting a male bunny because they have a tendency to be more affectionate and not as aggressive as females, especially if they are neutered. He also said that bunnies who are handled a lot when they are young are more comfortable being held and more affectionate around new people. When I picked Chip out, he wasn't as calm as some of the other bunnies, but he also didn't seem scared. He was curious and he would nip and nudge my hand. The breeder identified this behavior as playful. I liked him immediately. The only thing that concerned me was that he was squirmy when held but the breeder explained that with regular handling he'd come around.
I had Chip neutered when he was 4 months old. He is now 10 months old and seems to be a happy bunny, but also seems to get irritated easily. He has a lot of energy and is very playful, but he still does not like to be picked up. I have tried to get him used to this over the months but probably not hard enough because I was afraid it was stressing him out too much and it didn't seem to be getting better. I show him affection by petting him and talking softly and he'll lick me in response. But as soon as he thinks I might scoop him up, he runs away and thumps at me.
Recently, for seemingly no reason, he'll show signs of aggression. This includes running and hiding from me, thumping his hind legs and swatting me with his front paws and grunting when I try to reach in and pet him. The grunting scares me because I am afraid that he is really distressed when he does that. Sometimes he'll nip but never hard - enough to show me he's not happy. I don't know what is causing this. I thought maybe this was some kind of rebellious adolescent phase. I've tried to find a pattern in these "mood swings"- if a new person comes into my room, if I spend a night or two away from him, or if I have an argument on the phone. I try to be soothing but I don't know if I should just leave him alone. Any advice would be much appreciated. I love that little bunny and I want him to love me back!

Answer
Dear Stephanie,

The breeder who told you that Chip would "come around" if you handled him a lot was, like many rabbit breeders, completely clueless about rabbit nature.

MOST rabbits do not like being held, and it's against their nature to enjoy it.  A very few like it.  But they are the exception, not the rule.

The key to winning Chip's love and trust is to learn to speak more fluent "Rabbit."  This starts by interacting with him on his own terms, and not trying to pick him up, which he views as a threat.  Please read:

www.bio.miami.edu/hare/shybun.html

and for all the best information on general rabbit care and behavior:

www.rabbit.org

for tips on how to see the world through his eyes, and how to interact with him in a way that will instill trust.  

He sounds like a very intelligent bunny, and the smart ones are usually the most willful and willing to tell you what they like and DO NOT like.  :) He is communicating quite clearly that he does NOT like to be picked up (which is completely normal for a rabbit), and that he'd prefer you to interact with him as if you were another rabbit.  This can take some practice, but it's well worth it.  Soon you'll have your old pal back, and your bond will be stronger than ever.

Hope this helps.

Dana