Your larger cloud has a higher altitude, but what you have to realise, is that cloud depth works from the top down. I think.
So if a cloud has an altitude of 3000m, a depth of 1000m, the altitude at the base would be 2000m (3000-1000).
EDIT Actually I'm wrong according to your settings, although that's how I've been figuring it. If your cloud at 3000 metres has a depth of 4500m then 1500m of it would be underground. So looks like you're right.
Nice cloud shapes btw.