How old is he? Do you jump him full height or did fences?

What are the courses like you are trying to do? You need to stick to simple things like 3 jumps in a straight line with a pot of food at the end as a jackpot reward or a circle of jumps.
Do you clicker train? Maybe you could click and give a jackpot reward for any signs of enthusiasm.
My Bertie is laid back for a BC, he is retired from agility now, but when he competed I'd wind him up at the start, I wouldn't ask for a wait (he can and I sometimes would in competition if it was a difficult start that would be better if I got into position), then we'd run as fast as I could in front of him. He was particularly slow in weaves and I can remember 1 time I actually said ducks to him while he was in the weaves to speed him up a bit. He did win me out of Elementary and was in 3 finals, 2 at DINAS and 1 at Supadogs (my last ever Starters run as Teagan won me out), he also ended up in grade 4, getting a 6th place the year they split Novice, but that was a fluke as it was a difficult course and there were only 6 clear rounds!!! He's retired now as he's nearly 11 years old.
What do you do when he's slow? Do you 'cheerlead', clapping and vocally encouraging? This can actually have the opposite affect.

He's 3 and not doing full height. He's not doing anything complicated. We start with three in a straight line or one turn as a warm up and the most complicated thing he has done is diagonals, which aren't complicated at all to him because he's still jumping in a straight line.

When he is stood there looking at me I try and encourage him but I know if I go overboard it will have the opposite effect on him because he's quite sensitive.

I can use the clicker if he'll do something to earn a click but I can't click him for standing looking at me or wandering around sniffing. He's so complicated, I don't know what's going on in his head. I have lots of things to try now before we have our next lesson.

What do you do if he switches off? do you just stop or moveto something that you feel will motivate him?

Yes, we'll go and do the contact equipment or sometimes move on to a different set of jumps in a different area.

How about using the contact equiptment as a reward...(ie - do 3-4 jumps and are allowed to go over the aframe?)

He could be learning that if is does not do the jumps (boring stuff for him) he is moved to something he does like.

I would be tempted to only allow him to do the things he enjoys as a reward from doing some jumps. If he doesn't want to jump he doesn't get to play.

Good idea, thanks. I'll have to write all these suggestions down now before I forget!

I would deff make it even easier for him - one jump and if in any way does it good click, reward and go straight onto something he likes

and remember sniffing can be a displacment activity, if he is feeling stressed that you are asking too much of him or he dosent understand what you want

I totaly reward looking at me - focus is great (although not while we are actually running)

also what tricks does he know?? if not many then teach him some (have a look at our trick training challanges in the training section) and find out what tricks he likes, and how to motivate him doing tricks
Work on making things fun fun fun and take the pressure off

How about teaching directions and things just through the jump wings so he isnt even jumping at all??

and get him checked out to make sure there isnt a medical reason for him not wanting to jump

If he really has shut down I'll ask him to do a few things in a row like sit, down, high five, turn around and he does those with no hesitation, but ask him to jump again afterwards and he refuses. He'll jump over things out on our walks and jumps on park benches which is a trick I taught him when he was refusing the dogwalk so I know he doesn't mind jumping and once he starts and gets into a stride he's perfectly happy to carry on even if it means jumping what he doesn't need to! If he goes wrong I just carry on because stopping will switch him off, too.

I think asking him to sit and wait switches him off but I do need to get ahead of him sometimes so I can try stand and wait.