We have 4 cats. 2 males at 11 years old, 1 female 11 years old and a 10 month old kitten. For the first 6 months we had the kitten (Beau), he and my female (Monet) got along OK, not great, but they tolerated each other. For the last 3 weeks, however, Monet is scared to death of Beau and hisses, growls and runs away. Sometimes he catches her and beats her pretty badly, but mostly she makes it to a few high spots in the kitchen and my office to avoid him.
You wrote the following to another writer: "However, sometimes it's the other cat who has a problem and starts to cower and run away for whatever reason and just the act of acting scared and running away will make the other cat attack." Why is this? Why will the other cat (Beau in this case) attack?
By the way, I took Monet, my female cat, to the vet to see if there was a problem and she has elevated something in her liver so she's on Flagyl right now.
If your cat was ill around the time this started or even before this started, as it sounds she was, this alone can prompt aggression in other cats. Cats tend to have a sixth sense for sensing illnesses in other cats and can behave aggressively because of the instinct for survival of the fittest.
Frankly, cats may attack another cat that cowers in fear for the very same reason. It is instinct for a cat to go after those that appear weaker.
Also, in terms of your particular cat behavior problem, I would like to mention that unneutered males, as they come into adolescence, can become frisky with females (whether spayed or not) and sometimes even other male cats. If your kitten is not neutered, or if he was neutered late, this could be another contributing factor to your aggression problem.
For tips on how to help your cat behavior problems, please see this page on Fighting Cats.