What strikes me is the fact that she is going IMMEDIATELY when you put her in the crate. She may have a little separation anxiety going on. Is there a room that you can block off and puppy proof for when you leave? Like your kitchen? Depending on the size of her crate you could even leave it in the room you have blocked off and make it all cozy, leave the door open and lay some puppy pads or newspaper outside of it for her to go potty in. That way she doesn't have to sit in her mess and would more than likely go and snooze in her crate.
Just some thoughts.
