I have a lesson again monday and I plan on talking to her then, I'd even be willing to offer to get off and lower the fences for myself and raise them again for her through the entire lesson, until I'm comfortable moving up.
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No offence but I think this is a terrible idea. She is your instructor, you are paying her to instruct. You're not paying to climb up and down a horse fixing jumps. I'm going to be a little harsh here, but I think you are of a very much "victim" mentality right now, which is kind of ridiculous. You start of the thread by saying you were losing your confidence, only wanted to jump 2ft, and that the horse was crashing through the jump, and then said later on that you were enjoying 3ft jumps? Which is it? I don't think you, your coach or the horse is bad, but I think you have to get things straight in your head before you can attempt to fix the communication problem between you three, which there obviously is.
I don't think the height of the fences is really your problem. There isn't much between a 2ft and 3ft fence, you practically ride them the same, and if the horse is capable then there shouldn't be a problem. But if the horse is running out and plowing through jumps you should be going back to basics. Grids, moving off the leg etc. One of the best instructors I ever had taught me something I found really important - most training for any discipline is done on the flat. Once you perfect things on the flat, you just add fences and go over them. To me, jumping isn't about going over the fences, its the riding you do in between. So, if I were you, I'd go back to your flat work, maybe take a couple of weeks without jumping and get your stuff together. Something has obviously to make you uncomfortable, you know it, your horse knows it, and your coach probably guesses, work out what the problem is and fix it. And this may not even be a riding problem, it could be personal, you could have seen a car accident or watched a freaky movie that made your realise you're not invincible and suddenly that jump is too big. Don't just jump for the sake of it. My opinion is that if you're not fully confident you can get over that jump you have no business jumping it.
Someone on here mentioned respecting the instructor. Now I respect all human beings but I don't accept anything blindly. If someone is successful or educated in whatever I am learning I certainly will give their advice more weight, but that doesn't mean I just do whatever they say. Respect isn't doing whatever someone says. Coaches don't always know best, nor do teachers or parents or doctors. I know people who do these things, and they're not gods, they're not infallible, they make mistakes everyday, they misunderstand things, all of them have contradictory opinions and none of them are right all the time. Question what you're told, be honest about what you want and if your instructor isn't willing to offer you the service you want get a new one but if you're not upfront and honest about things you are going to have the same problems all over again. Don't blame other people or other things, tell them how it is, how you feel and work together from there.