Well... I too have the same issue at times w/ the pee pad, though not as much lately. Maybe you can try using a larger sized pad (which is something Im thinking of doing). Meka is 7 mo's now, and I know she knows where to go... But, sometimes when I watch her - as you stated, she'll move/smell around a few times before she goes... I also have a spray that I put on the pad - thats suppose to make them want to go...
As far as your pup peeing in her crate... Sounds like she's definately excited that your home. From my own exp and what Ive read on here, you have to let them calm down a little before you greet her. Hope this helps