welll it good you don't pay any attention when she whines,

the reason why she does not whine in her crate is because usally crates are like a safe place it has a top and it feels safe in there, also she can't see you moving around in the crate very easilly.

in the pen she can see you moving around alot and that upseting because she wants to be with her mommy, which you just need to keep on ignoring her and she will get the picture that, she will not get her way, she is just testing you keep it up! DOn't pay any attention to her, and then once she stops whining let her out, so she is awarded basically that she stoped whining! good luck puppy are hard, but there a joy, take advantage becaause they grow up fast.