I think this is not so much a barking problem, but a communication problem. She's trying to tell you she feels left out. Yorkies are definitely pack animals and like to be with the other members of the pack. I think some people just ignore the barking, and say it goes away in time; behavioral psychologist calls this extinction. Extinction is a behavior training technique where the animal gets no reward for its behavior. In other words, when it barks it never gets out of the playpen.
I could never do this. I would put Joey in his playpen for short amounts of time and tried to take him out before he barked, but as he got older he hated the pen unless I got in it with him. Punishing which is different than extinction usually isn't beneficial with this sort of problem.
I do think animals can "read" you, and if you feel guilty about having to put them in the pen while you get ready for work, they are going to bark even more. So once you have done what's best for your pup, and you know she's safe, just try to ignore the barking and don't feel guilty. Have you thought about a companion to keep her company while you're at work?
Anyway welcome to Yorkietalk!!
