As a web developer myself who has done pricing mechanisms like this, I usually charge a little less as a general rule to keep customers happy and coming back as well as spreading the word about me. You really shouldn't think about charging for as much as you can until you have more customers than you can handle.
Having said this, it really all depends on the circumstances surrounding your questions.
- If i have an IE/CSS issue that takes me an hour of scouring CSS to fix, is that chargeable?
Is this "issue" a bug in your coding? If so, you are obligated to fix your bugs at no additional charge. Or is this "issue" adding in a feature you really didn't know how to add in before starting your project? If so, I still wouldn't charge anything because you learned something from the experience and will be able to do it easily for your next customer. It's your fault that it took you an irregular amount of time to do, not your customer.
- If i decide to use a really cool jQuery animation on their site but i need to get to grips with using it, do i charge them for the experimenting i do with the animation. Do you charge customers for something that they ask for, that you dont know about and therefore need to spend time learning
Like I said for the first bullet, I personally wouldn't charge them for this since you learned something from this. Besides, the jQuery animation was your idea, not your customers. Unless you specifically told them prior to hiring that it would cost extra for you to do this because it is something that you do not normally do, it's not appropriate to charge extra for it in my opinion.
Based on your questions I would strongly recommend trying to agree on a price prior to creating your customers website; Even if it's just a price per hour. If they ask for additional features as you develop it then that is one of the few valid excuses to charge extra. Remember that your customer is paying you so that you can perform a service you enjoy doing and you are not trapped washing dishes to make money. If you treat them poorly and try to get as much out of them as you can they will figure it out and they will look elsewhere.
I hope this helps. Good luck down the road!