Rabbits definitely have changing moods and their body posture and behavior can "tell" you what their mood is at a given time. It could very well be that you happened to try to pet her when she wasn't in the mood to be bothered. Rabbits can be that way. So while she may have been all affection at one time of day, that doesn't mean she will be eager for affection later that same day. They prefer affection on
their terms.
You may want to do some research/reading on bunny body language so you can read those signs. Growling can be a warning that means 'stop what you are doing.' Ignoring it could result in a bite. Lunging is another warning to back off.
Also, where is she when you are petting her? It is best to not reach into the cage to pet a rabbit. I reserve petting for when bunny is out of the cage. Too much intrusion into their cage (their sanctuary) can encourage a rabbit to become "cage-aggressive" meaning they feel the need to protect their territory/space.
Rabbits need a space they can call their own, a place in which they know they will not be disturbed. The cage is often the best place for this.
Since she's showing signs of not liking your hand in her cage (eg. changing water) then at least for awhile, you may need to wait until she's out of the cage or distracted to do water changes or to add hay, etc.
Rabbits are finicky and moody. They aren't always eager for affection (the way a dog would be). So don't take these incidences personally. Your rabbit sounds like she's just being a rabbit -- ornery comes with the territory.
I'd also agree with samoth that 4 weeks is a very short time for a rabbit to get settled in. Give her time, patience, and read up on that bunny body language. Here's a link:
http://language.rabbitspeak.com/