Unfunny Bunny Behaviour

Question
Hello,
   my name is Andrwe Hudson, and have two rabbits and two cats.  My bunnies are kept in the garage in a very spacious cage, allowing them to run and jump and all that.  I even go in the cage to play with them! The cats are left in the main house, as they are better litter trained than the bunnies.  The bunnies are a mini rex named Lilly, and a half mini rex half dwarf named Misty.

   That was some back ground information.  The problem is Misty is a very confident rabbit, and is the 'boss'.  They used to get along very well, and it was very cute to see them cuddle up and everything.  But lately it seems Misty is more aggressive, and Lilly is far more timid and almost terrified of Misty at times.  Sometimes, if im giving attention to Lilly, Misty will run and chase Lilly, Lilly will make a whinning sound also.  Lilly doesnt really like being touched by me, but Misty does.  It kind of makes me sad, because I wanted bunnies to play with and that might sit in my lap and let me pet them... Stuff like that, but they seem to not be like that at all... I can accept the personalities, however I dont want Misty abusing Lilly, and I dont want Lilly to be scared of me.  I try really hard to be nice to them ( how can you not be nice to something that cute!?)... So any advice on how to handle their strange behavior would REALLY be appreciated... Thank you!
-Andrew

Answer
How old are these rabbits, and are they spayed or neutered?  The whining sound you are hearing sounds a lot like a sound that an unspayed female rabbit would make.  

If they are not spayed or neutered, you might read this article, http://www.rabbit.org/faq/sections/spay-neuter.html  

Also, you might check out this article about bonding difficulties, http://www.rabbit.org/journal/4-4/tough-bonding.html  

These would be the things I would think of first, so I hope that this helps you out.

Kim