I'm not Miriam...but...
For the small rears in succession...just spend more time rewarding each small one, until he's absolutely, positively sure what you want for that particular cue. Then ask for two. Reward. Then reward each one again. Then try three....then one, then one, then one, then two, etc.
But if he's offering different behaviors (or different heights in this case) then he's simply not sure that the low one is what you want. It's possible that by not rewarding each one, then he was within his operant conditioning rights to offer something different.
It just means he's not sure what you're rewarding for.
And I wouldn't throw anything else in the mix...duration, or elevation, until you are sure HE'S sure of what the first one means. But you'll have to find a cue that is novel enough not to confuse him with the low rear vs higher one. Maybe you add a touch of a whip under his rib cage to indicate height...or a touch on his legs to indicate duration...but repeated attemtps of the same behavior, and duration of a single behavior will be difficult for him to sort out. For that you must be patient and know that some confusion will occur.
But also...if you want to go back to classical roots...the levade...the low rear, is not a rear at all, but a lowering of the haunches with an elevated front end.
So I am spending a great deal of time with Tam, asking him to try and lower his haunches. This is stemming from the Goat, and the rein back, with just a touch of a lifted cordeo, to signal UP. But I'm clicking (as much as I can) before the front feet leave the ground...because I'm trying to isolate and reward for what the haunches are doing.
When Tam is strong enough to levade, simply holding the cordeo, back and up, should signal the duration.
When it comes to pesade, I will change the cues...I may ask for back and up, but not ask for the sit (which, by the way, can be cued with a touch of the whip on top of the butt).http://www.youtube.com/watch?v=2R8Jj68pB2A
Study the horse's movement in this video. He takes a step back to even his hind feet, then he sits back into the lifting of the front end.
This requires a lot of trust on the horse's part...and an understanding to keep the hind feet in place and not just back up...when he's asked to sit into the levade. So perhpas you can find your difference there...that the levade is a backward motion...the pesade and rear may be more upward...and when leading to capriole or some other air that requires forward movement...more forward?
I guess what I'm saying is that the cue may stem form where you want the movements to end up in their finished form...or think ahead enough to visualize what you might do with a movement once it's perfected. Where can it go from there? So a high rear might be both hands in the air, and at some point, you may be able to vibrate them to indicate duration, or move yourself forward to ask the horse to walk forward while rearing...or leaping forward while staying on the hind legs...while a levade or pesade may be a touch on the top of the rump, along with a hand gesture to indicate height, or the raising and lowering and raising again of the front end.
Now isn't that a confusing mess I just typed? I'm too tired to edit it!